Molecular evidence that the capacity for endosporulation is universal among phototrophic heliobacteria

Although enrichment cultures for anoxygenic phototrophic heliobacteria commonly contain sporulating cells, once strains of heliobacteria are obtained in pure culture, they all but cease to sporulate. In fact, some species of heliobacteria have never been observed to sporulate. Thus, despite their phylogenetic connection to endospore-forming bacteria, the question of sporulation capacity in heliobacteria remains open. We have investigated this problem using PCR and Southern hybridization as tools and show here that all recognized species of heliobacteria tested, as well as several unclassified strains, contain homologs to the ssp genes of Clostridium and Bacillus species, genes that encode key sporulation-specific proteins. It can therefore be concluded that as a group, heliobacteria are likely all to be endospore-forming bacteria in agreement with their phylogenetic placement within the 'low GC' Gram-positive bacteria.     

BIOCHEMICAL CHANGES IN YEAST DURING SPORULATION. II. ACETATE METABOLISM

Acetate metabolism was studied with Saccharomyces cerevisiae diploid strain G2-2 in sporulating culture, asporogenic diploid strains 3c × a and 3c × 3a, and respiratory deficient haploid strain 3c (asporogenic). Acetate in a sporulating medium was utilized by sporogenic and asporogenic diploid yeasts linearly with time. Activities of aconitase, NADP-linked isocitrate dehydrogenase, and succinate dehydrogenase initially increased in the cell-free homogenate of either strain. Activity of glucose-6-phosphate dehydrogenase decreased. Isocitrate lyase activity increased remarkably in the sporogenic strain but not in the asporogenic strain. The rate of production of ¹⁴CO₂ from ¹⁴C-1-acetate was accelerated more than from ¹⁴C-2-acetate in intact cells of the sporogenic strain during sporulating culture. Fractionation of radioactive cell substances showed remarkable lipid synthesis. Accumulation and reutilization of cold acid-soluble precursor substances occurred during sporogenesis. The role of glyoxylate and tricarboxylate cycle enzymes in sporulation is discussed.     

Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901

We report here the sequencing and analysis of the genome of the thermophilic bacterium Carboxydothermus hydrogenoformans Z-2901. This species is a model for studies of hydrogenogens, which are diverse bacteria and archaea that grow anaerobically utilizing carbon monoxide (CO) as their sole carbon source and water as an electron acceptor, producing carbon dioxide and hydrogen as waste products. Organisms that make use of CO do so through carbon monoxide dehydrogenase complexes. Remarkably, analysis of the genome of C. hydrogenoformans reveals the presence of at least five highly differentiated anaerobic carbon monoxide dehydrogenase complexes, which may in part explain how this species is able to grow so much more rapidly on CO than many other species. Analysis of the genome also has provided many general insights into the metabolism of this organism which should make it easier to use it as a source of biologically produced hydrogen gas. One surprising finding is the presence of many genes previously found only in sporulating species in the Firmicutes Phylum. Although this species is also a Firmicutes, it was not known to sporulate previously. Here we show that it does sporulate and because it is missing many of the genes involved in sporulation in other species, this organism may serve as a “minimal” model for sporulation studies. In addition, using phylogenetic profile analysis, we have identified many uncharacterized gene families found in all known sporulating Firmicutes, but not in any non-sporulating bacteria, including a sigma factor not known to be involved in sporulation previously.     

The program of protein synthesis during sporulation in Bacillus subtilis

The program of protein synthesis was examined during sporulation in Bacillus subtilis as an index of the control of gene expression. At various stages of growth and spore formation, cells of B. subtilis were pulse-labeled with ³⁵S-methionine. Protein was extracted from the radioactively labeled bacteria and then subjected to high resolution one-dimensional and two-dimensional slab gel electrophoresis. We report that sporulating cells restricted or “turned off” the synthesis of certain polypeptides characteristic of the vegetative phase of growth. In certain cases, this “turn off” was prevented in a mutant (SpoOa-5NA) blocked at the first stage of spore formation. Sporulating bacteria also elaborated new polypeptide species that could not be detected in vegetatively growing cells or in cells of the asporogenous mutant SpoOa-5NA in sporulation medium. The synthesis of these sporulation-specific proteins was “turned on” in a temporally defined sequence throughout the period of spore formation. Spore coat protein, for example, was first synthesized at 4 hr after the onset of sporulation, the time at which refractile prespores appeared. Certain sporulation-specific polypeptides including the coat protein were among the most actively produced polypeptides in sporulating cells.     

Studies on the nature and role of polyadenylated RNA in spore development of Bacillus subtilis

Summary cDNA probes synthesized on poly(A)RNAs isolated from sporulating cells of Bacillus subtilis were used for hybridization studies with RNAs derived from cells at different stages of growth and sporulation. It was shown that these cDNAs hybridized only to RNA from sporulating cells. No hybridization was observed if total RNA isolated from vegetative cells or from stationary phase cells of a zero stage asporogenic mutant was used. The hybridization studies also indicate that at each sporulation stage different poly(A)RNA species are synthesized. Furthermore, the hybridization kinetics have clearly demonstrated the existence of three distinct abundance classes of poly(A)RNA similar to those observed in eukaryotic cells. BamHI endonuclease restriction fragments of B. subtilis DNA that were found to hybridize to labeled poly(A)RNA were ligated to the pHV33 vector and hybrid clones that hybridized efficiently to poly(A)RNA were selected. Among these, three have been found to carry the spoOB gene.These results strongly suggest that the appearance of poly(A)RNA can be correlated to the expression of spore genes.     

Regulation of gene expression during meiosis in Saccharomyces cerevisiae: SPR3 is controlled by both ABFI and a new sporulation control element.

The SPR3 gene encodes a sporulation-specific homolog of the yeast Cdc3/10/11/12 family of bud neck filament proteins. It is expressed specifically during meiosis and sporulation in Saccharomyces cerevisiae. Analysis of the sporulation-specific regulation of SPR3 has shown that it is strongly activated under sporulating conditions but shows low levels of expression under nonsporulating conditions. A palindromic sequence located near the TATA box is essential to the developmental regulation of this gene and is the only element directly activating SPR3 at the right time during sporulation. Within the palindrome is a 9-bp sequence, gNCRCAAA(A/T) (midsporulation element [MSE]), found in the known control regions of three other sporulation genes. A previously identified ABFI element is also needed for activation. The MSE has been shown to activate a heterologous promoter (CYC1) in a sporulation-specific manner. Related sequences, including an association of MSE and ABFI elements, have been found upstream of other genes activated during the middle stage of S. cerevisiae sporulation. One group of these may be involved in spore coat formation or maturation.     

A genomic update on clostridial phylogeny: Gram‐negative spore formers and other misplaced clostridia

The class Clostridia in the phylum Firmicutes (formerly low‐G+C Gram‐positive bacteria) includes diverse bacteria of medical, environmental and biotechnological importance. The Selenomonas‐Megasphaera‐Sporomusa branch, which unifies members of the Firmicutes with Gram‐negative‐type cell envelopes, was recently moved from Clostridia to a separate class Negativicutes. However, draft genome sequences of the spore‐forming members of the Negativicutes revealed typically clostridial sets of sporulation genes. To address this and other questions in clostridial phylogeny, we have compared a phylogenetic tree for a concatenated set of 50 widespread ribosomal proteins with the trees for beta subunits of the RNA polymerase (RpoB) and DNA gyrase (GyrB) and with the 16S rRNA‐based phylogeny. The results obtained by these methods showed remarkable consistency, suggesting that they reflect the true evolutionary history of these bacteria. These data put the Selenomonas‐Megasphaera‐Sporomusa group back within the Clostridia. They also support placement of Clostridium difficile and its close relatives within the family Peptostreptococcaceae; we suggest resolving the long‐standing naming conundrum by renaming it Peptoclostridium difficile. These data also indicate the existence of a group of cellulolytic clostridia that belong to the family Ruminococcaceae. As a tentative solution to resolve the current taxonomical problems, we propose assigning 78 validly described Clostridium species that clearly fall outside the family Clostridiaceae to six new genera: Peptoclostridium, Lachnoclostridium, Ruminiclostridium, Erysipelatoclostridium, Gottschalkia and Tyzzerella. This work reaffirms that 16S rRNA and ribosomal protein sequences are better indicators of evolutionary proximity than phenotypic traits, even such key ones as the structure of the cell envelope and Gram‐staining pattern.     

In Vivo and In Vitro Function of the Intracellular Proteolytic Apparatus in Nongrowing Bacillus megaterium Under Heat Stress

In Bacillus megaterium sporulating at 35°C, up to 90% of 10-min pulse-labeled proteins were degraded. Degradation proceeded in two waves. Short-lived proteins, i.e., intrinsically labile proteins and proteins made short-lived because of starvation, were mostly degraded during the reversible sporulation phase. Their amount corresponded to 20% or slightly more during 2 h. The second wave of protein degradation, which followed during the irreversible sporulation phase at 35°C, increased the amount of total degradable pulse-labeled proteins to about 90%. This wave was absent in the isogenic asporogenic mutant 27-36 or in the wild strain, whose sporulation was inhibited by increased temperature. The proportion of degradable proteins was thus reduced to less than 40% in the asporogenic mutant incubated at 35°C and to 46% in the wild strain whose sporulation was suppressed by the temperature of 47°C. Unlike sporulating cells, these cells were thus capable of degrading short-lived and denatured proteins, but were not able to degrade most of other proteins. The in vitro protein degradation was substantially enhanced by increasing the Ca²⁺ concentration, suggesting a role of Ca²⁺-dependent proteinase(s) in the process. Received: 23 July 1998 / Accepted: 19 August 1998     

The isolation of heavy-metal resistant culturable bacteria and resistance determinants from a heavy-metal-contaminated site

In this study we performed a phylogenetic analysis of a culturable bacterial community isolated from heavymetal-contaminated soil from southwest Slovakia using 16S rRNA (16S rDNA) and heavy-metal resistance genes. The soil sample contained high concentrations of nickel (2,109 mg/kg), cobalt (355 mg/kg) and zinc (177 mg/kg), smaller concentrations of iron (35.75 mg/kg) and copper (32.2 mg/kg), and a trace amount of cadmium (<0.25 mg/kg). A total of 100 isolates were grown on rich (Nutrient agar No. 2) or minimal (soil-extract agar medium) medium. The isolates were identified by phylogenetic analysis using partial sequences of their 16S rRNA (16S rDNA) genes. Representatives of two broad taxonomic groups, Firmicutes and Proteobacteria, were found on rich medium, whereas four taxonomic groups, Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria, were represented on minimal medium. Forty-two isolates grown on rich medium were assigned to 20 bacterial species, while 58 bacteria grown on minimal medium belonged to 49 species. Twenty-three isolates carried czcA- and/or nccA-like heavy-metal-resistance determinants. The heavy-metalresistance genes of nine isolates were identified by phylogenetic analysis of their protein sequences.     

Induction of trehalase activity on a nitrogen-free medium: a sporulation-specific event in the fission yeast, Schizosaccharomyces pombe

Summary Kinetic experiments with synchronously sporulating cultures of a homothallic h⁹⁰ strain of Schizosaccharomyces pombe showed that trehalase activity abruptly increased in the late sporulation process, coinciding with the appearance of visible spores. Trehalase activity was absent in vegetative cells. A set of strains different in genetic constitution at the mating type loci was tested for induction of trehalase on nitrogen-free sporulation medium. The appearance of trehalase activity on the sporulation medium was observed only in sporulating cultures; cultures of homothallic strains (h⁹⁰) and diploid strains heterozygous for mating type (h⁺/h^–), and mixed cultures of heterothallic h⁺ and h^– strains. Trehalase activity was not induced in nonsporogenic strains: heterothallic haploid strains (h⁺ and h^–), diploid strains homozygous for mating type (h⁺/h⁺ and h^–/h^–) and the homothallic strain harboring the mutation in the mat2 gene, which was unable to undergo the first meiotic division. Trehalose accumulation on the sporulation medium was observed solely in the sporulating cultures. These results led us to conclude that the induction of trehalase activity as well as the accumulation of trehalose in the medium lacking nitrogen sources was a sporulation-specific event under the control of the mating type genes.     

Phylogeny and molecular fingerprinting of green sulfur bacteria

The 16S rDNA sequences of nine strains of green sulfur bacteria (Chlorobiaceae) were determined and compared to the four known sequences of Chlorobiaceae and to sequences representative for all eubacterial phyla. The sequences of the Chlorobiaceae strains were consistent with the secondary structure model proposed earlier for Chlorobium vibrioforme strain 6030. Similarity values > 90.1% and K_nuc values < 0.11 indicate a close phylogenetic relatedness among the green sulfur bacteria. As a group, these bacteria represent an isolated branch within the eubacterial radiation. In Chlorobiaceae, a similar morphology does not always reflect a close phylogenetic relatedness. While ternary fission is a morphological trait of phylogenetic significance, gas vesicle formation occurs also in distantly related species. Pigment composition is not an indicator of phylogenetic relatedness since very closely related species contain different bacteriochlorophylls and carotenoids. Two different molecular fingerprinting techniques for the rapid differentiation of Chlorobiaceae species were investigated. The 16S rDNA fragments of several species could not be separated by denaturing gradient gel electrophoresis. In contrast, all strains investigated during the present work gave distinct banding patterns when dispersed repetitive DNA sequences were used as targets in PCR. The latter technique is, therefore, well suited for the rapid screening of isolated pure cultures of green sulfur bacteria. Received: 26 August 1996 / Accepted: 8 January 1997     

Characterization of the predominant bacterial population of different mangrove rhizosphere soils using 16S rRNA gene-based single-strand conformation polymorphism (SSCP)

Variations in chemical parameters and bacterial populations in mangrove rhizosphere samples were noted for different sites. The C, N, P and K contents as well as pH, EC and salinity showed variation between sites. Significant differences in soil properties were also found in sampling sites. Two types of soil were noted among sites. Guesthouse had significantly higher organic matter and nutrient content (N) than other three sites suggesting that human discharges, litter deposition and surface runoff were major nutrient inputs. This contaminated site was located at the landward edges. Positive correlations between organic matter, N, P and K contents were found suggesting that these nutrients were from similar input sources. Effects of sampling sites on microbial diversity were also analyzed via SSCP. Porteresia coarctata and Rhizophora mucronata did not show any variation in the banding patterns among replicates sampled in short distance within site. But Sonneratia apetala showed variation among replicates sampled in distance within site. A significant variation was noted in the SSCP profile among replicates between sites. The majority of dominant SSCP band sequences were related to bacterial genera of root and root-free soil environments, namely Bacillus, Planococcus, Planomicrobium, low G+C Gram-positive bacterium, glacial ice bacterium and unidentified bacteria. In the analysis of 16S rRNA sequences, members belonging to the phylum Firmicutes dominated the sequence collection. The phylogenetic analysis of 16S rRNA gene sequences showed close relationships to a wide range of clones or bacterial species of phylum Firmicutes and unidentified bacteria.     

醋酸菌中CRISPR位点的比较基因组学与进化分析

CRISPR (Clustered regularly interspaced short palindromic repeats)是近几年发现的一种广泛存在于细菌和古菌中,能够应对外源DNA干扰(噬菌体、病毒、质粒等),并提供免疫机制的重复序列结构。CRISPR系统通常由同向重复序列、前导序列、间隔序列和CRISPR相关蛋白组成。本研究以醋酸发酵中常见3个属醋杆菌属(Acetobacter)、葡糖醋杆菌属(Gluconacetobacter)和葡糖杆菌属(Gluconobacter)的48个菌株为研究对象,通过其基因组上CRISPR相关基因序列的生物信息学分析,探索CRISPR位点在醋酸菌中的多态性及其进化模式。结果表明48株醋酸菌中有32株存在CRISPR结构,大部分CRISPR-Cas结构属于type I-E和type I-C类型。除了葡糖杆菌属外,葡糖醋杆菌属和醋杆菌属中的部分菌株含有II类的CRISPR-Cas系统结构(CRISPR-Cas9)。来自不同属菌株的CRISPR结构中重复序列具有较强的保守性,而且部分菌株CRISPR结构中的前导序列具有保守的motif (与基因的转录调控有关)及启动子序列。进化树分析表明cas1适合用于醋酸菌株的分类,而不同菌株间cas1基因的进化与重复序列的保守性相关,预示它们可能受相似的功能选择压力。此外,间隔序列的数量与噬菌体数量及插入序列(Insertion sequence, IS)数量有正相关的趋势,说明醋酸菌在进化过程中可能正不断受新的外源DNA入侵。醋酸菌中CRISPR结构位点的分析,为进一步研究不同醋酸菌株对醋酸胁迫耐受性差异及其基因组稳定性的分子机制奠定了基础。     

Expression of parasporal crystal protein (δ—endotoxin) gene(s) ofBacillus thuringiensis var.israelensis in sporogenic and asporogenic mutant strains ofBacillus cereus

The expression of parasporal crystal protein (δ-endotoxin) coding gene(s) ofBacillus thuringlensis var.israelensis and its association, if any, with sporulation was studied in sporogenicBacillus cereus and its asporogenic mutant strains. Five asporogenous mutants ofBacillus cereus blocked at different stages of sporulation, were isolated from a streptomycin-resistant strain, The transconjugants isolated from the plasmid transfer experiments betweenBacillus thuringiensis var.israelensis and streptomycin resistantBacillus cereus and its asporogenous mutants, showed larvicidal activity. The crystal protein gene(s) are, therefore, expressed both in sporulating and in non-sporulating mutant strains ofBacillus cereus suggesting that the expression of crystal protein gene(s), is independent of sporulation specific functions inBacillus cereus. Part of the work was carried out at Biotechnology Programme, Jadavpur University, Calcutta 700 032, India.     

A novel taxonomic marker that discriminates between morphologically complex actinomycetes

In the era when large whole genome bacterial datasets are generated routinely, rapid and accurate molecular systematics is becoming increasingly important. However, 16S ribosomal RNA sequencing does not always offer sufficient resolution to discriminate between closely related genera. The SsgA-like proteins are developmental regulatory proteins in sporulating actinomycetes, whereby SsgB actively recruits FtsZ during sporulation-specific cell division. Here, we present a novel method to classify actinomycetes, based on the extraordinary way the SsgA and SsgB proteins are conserved. The almost complete conservation of the SsgB amino acid (aa) sequence between members of the same genus and its high divergence between even closely related genera provides high-quality data for the classification of morphologically complex actinomycetes. Our analysis validates Kitasatospora as a sister genus to Streptomyces in the family Streptomycetaceae and suggests that Micromonospora, Salinispora and Verrucosispora may represent different clades of the same genus. It is also apparent that the aa sequence of SsgA is an accurate determinant for the ability of streptomycetes to produce submerged spores, dividing the phylogenetic tree of streptomycetes into liquid-culture sporulation and no liquid-culture sporulation branches. A new phylogenetic tree of industrially relevant actinomycetes is presented and compared with that based on 16S rRNA sequences.     

Bacterial, archaeal, and eukaryal diversity in the intestines of Korean people

The bacterial, archaeal, and eukaryal diversity in fecal samples from ten Koreans were analyzed and compared by using the PCR-fingerprinting method, denaturing gradient gel electrophoresis (DGGE). The bacteria all belonged to the Firmicutes and Bacteroidetes phyla, which were known to be the dominant bacterial species in the human intestine. Most of the archaeal sequences belonged to the methane-producing archaea but several halophilic archarea-related sequences were also detected unexpectedly. While a small number of eukaryal sequences were also detected upon DGGE analysis, these sequences were related to fungi and stramenopiles (Blastocystis hominis). With regard to the bacterial and archaeal DGGE analysis, all ten samples had one and two prominent bands, respectively, but many individual-specific bands were also observed. However, only five of the ten samples had small eukaryal DGGE bands and none of these bands was observed in all five samples. Unweighted pair group method and arithmetic averages clustering algorithm (UPGMA) clustering analysis revealed that the archaeal and bacterial communities in the ten samples had relatively higher relatedness (the average Dice coefficient values were 68.9 and 59.2% for archaea and bacteria, respectively) but the eukaryal community showed low relatedness (39.6%).     

Hydrogen production potential of fermentative microorganisms from the Sargasso Sea

Mounting evidence suggests that ammonia-oxidizing archaea (AOA) may play important roles in nitrogen cycling in geothermal environments. In this study, the diversity, distribution and ecological significance of AOA in terrestrial hot springs in Kamchatka (Far East Russia) were explored using amoA genes complemented by analysis of glycerol dialkyl glycerol tetraethers (GDGTs) of archaea. PCR amplification of functional genes (amoA) from AOA and ammonia-oxidizing bacteria (AOB) was performed on microbial mats/streamers and sediments collected from three hot springs (42°C to 87°C and pH 5.5-7.0). No amoA genes of AOB were detected. The amoA genes of AOA formed three distinct phylogenetic clusters with Cluster 3 representing the majority (～59%) of OTUs. Some of the sequences from Cluster 3 were closely related to those from acidic soil environments, which is consistent with the predominance of low pH (<7.0) in these hot springs. Species richness (estimated by Chao1) was more frequently higher at temperatures below 75°C than above it, indicating that AOA may be favored in the moderately high temperature environments. Quantitative PCR of 16S rRNA genes showed that crenarchaeota counted for up to 80% of total archaea. S-LIBSHUFF separated all samples into two phylogenetic groups. The profiles of GDGTs were well separated among the studied springs, suggesting a spatial patterning of archaeal lipid biomarkers. However, this patterning did not correlate significantly with variation in archaeal amoA, suggesting that AOA are not the predominant archaeal group in these springs producing the observed GDGTs.