Genome sizes and chromosomes in the basal metazoan Hydra

Hydras belong to one of the earliest eumetazoan animal groups, but to date very little is known about their genome sizes, gene numbers, and chromosomes. Here we provide genome size estimates and corresponding karyotypes for five Hydra species. Nuclear DNA contents were assessed by slide-based Feulgen microphotometry. Hydra oligactis possesses the largest genome of 1450 Mbp, followed by similar 1 C capacities in H. carnea (1350 Mbp), H. vulgaris (1250 Mpb) and H. circumcincta (1150 Mbp). The smallest genome of 380 Mbp was determined in H. viridissima. While the number of chromosomes is identical in all five Hydra species (2n = 30), the size of the chromosomes is strictly correlated to the size of the genome, with H. viridissima having conspicuously small chromosomes. The taxonomic and evolutionary significance of the C-value and chromosomal size variation in this ancient group of metazoans as well as its impact on genomic organization and forthcoming genome projects are discussed.     

Product inhibition ofTrichoderma reesei andCellulomonas glycosidase activities

Summary A comparison has been made of the effects of glucose, xylose and arabinose on the ability ofTrichoderma reesei andCellulomonas preparations to hydrolyse the glycosides of these three sugars. The stronger resistance of theCellulomonas preparations to product inhibition meant that these were comparable to theT.reesei preparations in the presence of 500mM sugar product.     

A thermostable endo-1,4-/B-glucanase from Myceliophthora thermophila

Summary Endo-1,4-/B-glucanase from a thermophilic fungusMyceliophthora thermophila has been isolated and purified to homogeneity. The molecular weight of the enzyme was 52,000 with a pI of 4.7, pH-optimum 5.0–6.0, and specific activity 61 IU/mg (40°, pH 5.0); this activity is 2.4 times higher than that of the enzyme fromTrichoderma reesei. The new endoglucanase is very thermostable; its half-life at 65°C is 170 hours, which is 300 times higher than that of the enzyme fromT. reesei.     

REPLICATION OF CHLORELLA VIRUS PBCV-1 AND HOST KARYOTYPE DETERMINATION STUDIED WITH PULSED-FIELD GEL ELECTROPHORESIS1

We demonstrated the time-course of DNA replication of the 330-kbp Chlorella virus PBCV-1 by pulsed-field gel electrophoresis. Viral DNA replication began between 90 and 120 min postinfeclion in cell samples produced without first removing cell walls. The host nuclear genome was degraded beginning almost immediately after infection, but some host DNA remained even after 360 min postinfection. The karyotype of the host alga consisted of nine resolvable bands that we presume to represent 13 chromosomes based on band intensity. The chromosomes ranged in size from 1.1 to 6.5 megabase pairs (Mbp). A summation of the sizes of the bands predicts a genome size of 39–45 Mbp of DNA.     

Electrophoretic karyotype and gene assignment to resolved chromosomes of Trichoderma spp.

A molecular karyotype for three different Trichoderma species (T. harzianum, T. viride, and T. reesei) was determined by using two different systems: countour-clamped electric-field and rotating-electrode electrophoresis. Six chromosomal DNA bands were observed in T. harzianum and T. reesei and five in T. viride. The sizes of these molecules were estimated by their mobility relative to the Schizosaccharomyces pombe chromosomes and ranged between 2.2 and 7.4 megabase pairs (mbp). The estimated genome sizes range from 31 to 39 mbp. A number of genes were located in the different chromosomes by means of Southern analysis. The implications of these findings are discussed.     

The expected nucleotide sequence of the human genome should be shortened about twofold

The sizes of nucleotide sequences of chromosomes 21 and 22 of the human genome established in three independent laboratories were compared with the sizes expected from the accurately determined contribution of these chromosomes to the genome mass. It was found that the expected haploid mass of the genome is about twofold smaller than the lowest of the figures published. This strongly contradicts the current notions about the genome size. With the bineme model of chromosome, the expected overall length of the human genome is close to 2100 Mbp and the haploid mass is close to 4200 Mbp. According to the calculations performed, the bineme chromosome structure enhances the reliability of the genome about 1.6 x 10(8)-fold (the computations are given in the paper).     

Thermostable tryptophan synthase ofBacillus stearothermophilus expressed inEscherichia coli

Summary The tryptophan synthase genes,trpA andtrpB, from a moderate thermophile,Bacillus stearothermophilus IFO13737, were expressed efficiently inEscherichia coli. The recombinant tryptophan synthase amounted to 22% of the soluble cellular protein, and was purified to homogeneity by three steps. The enzyme is more thermostable thanE.coli tryptophan synthase, especially the subunit. The enzyme is also more resistant to sodium dodecylsulfate and methanol thanE.coli enzyme.     

Enhanced cellulase production using Solka Floc in a fed-batch fermentation

Summary Use of a fed-batch mode of cultivation of T. reesei has permitted high concentrations of substrate to be consumed. This has resulted in the production of high titre cellulase preparations around 30 FPU/ml at high volumetric productivities (177 IU/L.hr).Perhaps the most obvious area for major improvement in the process of cellulose utilization is the production of cellulase enzyme for hydrolysis of wood and agricultural residues. It has been estimated that some 50% of the cost of producing glucose from cellulosic material is attributable to enzyme production alone (Perez, et al., 1980). Improvements in the area would therefore have a dramatic impact, and are of paramount importance if economical hydrolysis processes are to be realized. The first major thrust in the area has been the development of improved mutant strains of T. reesei, free from catabolite repression and capable of constitutive cellulase production (Montenecourt and Eveleigh, 1977; Gallo, 1982).While this effort continues to develop further high yielding mutants, improvement must also come from developments in fermentation techniques. A major advance is the use of fed-batch cultivation, which provides a means of avoiding the agitation and aeration difficulties, as well as repression effects encountered with high substrate concentration batch fermentation. This report briefly compares batch and fed-batch operation over a range of substrate concentrations.     

Chrysonila sitophila (TFB-27441): A hyperlignolytic strain

Summary C. sitophila strain TFB-27441 showed 2–3 times higher lignolytic activity thanPhanerochaete chrysosporium (BKM-F-1767 strain). Lignin had a marked effect on the ligninase activity indicating that some induction or activation mechanism is involved in lignin degradation byC. sitophila.     

Callus culture as substrate for the production of specific cell wall degrading enzymes for derived protoplast isolation

Callus culture of spruce (Picea excelsa LINK) appears to be a suitable substrate for the fungusTrichoderma reesei to produce an efficient extracellular lytic system for protoplast isolation. In comparison with Onozuka R-10 cellulase, a yield of protoplasts from the spruce callus 2·5 higher was obtained. Another testea commercial cellulase DK was less efficient. The addition of Macerozyme R–10 significantly enhanced release of protoplasts within all tested enzyme preparations. No difference in the viability of protoplasts has been observed.     

Genomic characterization of Neoparamoeba pemaquidensis (Amoebozoa) and its kinetoplastid endosymbiont

We have performed a genomic characterization of a kinetoplastid protist living within the amoebozoan Neoparamoeba pemaquidensis. The genome of this "Ichthyobodo-related organism" was found to be unexpectedly large, with at least 11 chromosomes between 1.0 and 3.5 Mbp and a total genome size of at least 25 Mbp.     

Selection of preculture conditions for solid state fermentation of sugar beet pulp

Summary For the protein upgrading of sugar-beet pulp in solid state fermentation byTrichoderma reesei andFusarium oxysporum, serveral conditions were studied to prepare an economical preculture for large scale process. The best performance was shown by a preculture obtained in 24 h from 1.5 % molasses solution at pH 4.5–5.0 with 1.0 % milled beet pulp.     

Genome and Chromosome Dimensions of Lotus japonicus

Lotus Japonicus , Miyakojima MG-20 and Gifu B-129. The genome sizes of Miyakojima and Gifu were determined as 472.1 and 442.8 Mbp, respectively. Both the accessions were diploid (2n=12) and six chromosomes were identified and characterized based on the condensation patterns and the locations of rDNA loci. The obvious polymorphism observed in the genome size and the chromosome morphology between the two accessions, revealed specific accumulation of heterochromatin in Miyakojima or elimination in Gifu. The chromosomes L. japonicus were numbered according to their length. A quantitative chromosome map was also developed by the imaging methods using the digital data of the condensation pattern. 45S rDNA loci were localized on chromosomes A and F, and 5S rDNA locus was localized on chromosome A by fluorescence in situ hybridization (FISH). Identification of the chromosome and genome sizes and development of the quantitative chromosome map represent significant contribution to the L. japonicus genome project as the basic information. Received 29 August 2000/ Accepted in revised form 17 October 2000     

Mis-Assembled "Segmental Duplications" in Two Versions of the Bos taurus Genome

We analyzed the whole genome sequence coverage in two versions of the Bos taurus genome and identified all regions longer than five kilobases (Kbp) that are duplicated within chromosomes with >99% sequence fidelity in both copies. We call these regions High Fidelity Duplications (HFDs). The two assemblies were Btau 4.2, produced by the Human Genome Sequencing Center at Baylor College of Medicine, and UMD Bos taurus 3.1 (UMD 3.1), produced by our group at the University of Maryland. We found that Btau 4.2 has a far greater number of HFDs, 3111 versus only 69 in UMD 3.1. Read coverage analysis shows that 39 million base pairs (Mbp) of sequence in HFDs in Btau 4.2 appear to be a result of a mis-assembly and therefore cannot be qualified as segmental duplications. UMD 3.1 has only 0.41 Mbp of sequence in HFDs that are due to a mis-assembly.     

Flow cytometry reveals that the rust fungus,Uromyces bidentis (Pucciniales), possesses the largest fungal genome reported—2489 Mbp

Among the Eukaryotes, Fungi have relatively small genomes (average of 44.2 Mbp across 1850 species). The order Pucciniales (Basidiomycota) has the largest average genome size among fungi (305 Mbp), and includes the two largest fungal genomes reported so far (Puccinia chrysanthemi and Gymnosporangium confusum, with 806.5 and 893.2 Mbp, respectively). In this work, flow cytometry was employed to determine the genome size of the Bidens pilosa rust pathogen, Uromyces bidentis. The results obtained revealed that U. bidentis presents a surprisingly large haploid genome size of 2489 Mbp. This value is almost three times larger than the previous largest fungal genome reported and over 50 times larger than the average fungal genome size. Microscopic examination of U. bidentis nuclei also showed that they are not as different in size from the B. pilosa nuclei when compared with the differences between other rusts and their host plants. This result further reinforces the position of the Pucciniales as the fungal group with the largest genomes, prompting studies addressing the role of repetitive elements and polyploidy in the evolution, pathological specialization and diversity of fungal species.     

Evolution of genome size and chromosome number in the carnivorous plant genus Genlisea (Lentibulariaceae), with a new estimate of the minimum genome size in angiosperms

MethodsNuclear genome sizes were measured from cultivated plant material for a comprehensive sampling of taxa, including nearly half of all species of Genlisea and representing all major lineages. Flow cytometric measurements were conducted in parallel in two laboratories in order to compare the consistency of different methods and controls. Chromosome counts were performed for the majority of taxa, comparing different staining techniques for the ultrasmall chromosomes.ConclusionsGenlisea is an ideal candidate model organism for the understanding of genome reduction as the genus includes species with both relatively large (∼1700 Mbp) and ultrasmall (∼61 Mbp) genomes. This comparative, phylogeny-based analysis of genome sizes and karyotypes in Genlisea provides essential data for selection of suitable species for comparative whole-genome analyses, as well as for further studies on both the molecular and cytogenetic basis of genome reduction in plants.     

Genome sequence analyses of two isolates from the recent <Emphasis Type="Italic">Escherichia coli</Emphasis> outbreak in Germany reveal the emergence of a new pathotype: Entero-Aggregative-Haemorrhagic <Emphasis Type="Italic">Escherichia coli</Emphasis> (EAHEC)

The genome sequences of two Escherichia coli O104:H4 strains derived from two different patients of the 2011 German E. coli outbreak were determined. The two analyzed strains were designated E. coli GOS1 and GOS2 (German outbreak strain). Both isolates comprise one chromosome of approximately 5.31 Mbp and two putative plasmids. Comparisons of the 5,217 (GOS1) and 5,224 (GOS2) predicted protein-encoding genes with various E. coli strains, and a multilocus sequence typing analysis revealed that the isolates were most similar to the entero-aggregative E. coli (EAEC) strain 55989. In addition, one of the putative plasmids of the outbreak strain is similar to pAA-type plasmids of EAEC strains, which contain aggregative adhesion fimbrial operons. The second putative plasmid harbors genes for extended-spectrum β-lactamases. This type of plasmid is widely distributed in pathogenic E. coli strains. A significant difference of the E. coli GOS1 and GOS2 genomes to those of EAEC strains is the presence of a prophage encoding the Shiga toxin, which is characteristic for enterohemorrhagic E. coli (EHEC) strains. The unique combination of genomic features of the German outbreak strain, containing characteristics from pathotypes EAEC and EHEC, suggested that it represents a new pathotype Entero-Aggregative-Haemorrhagic E scherichia c oli (EAHEC).     

Enhancingin vitro antibody production rate per cell by applying mouse peritoneal factors

Summary Monoclonal antibody production rateper hybridoma cell was measured as much larger in mouse peritoneal cavity thanin vitro culture. To identify factors enhancing antibody productivity per cell, a hybridoma was culturedin vitro with ascites and peritoneal exudate cells(PEC). Both the ascites and the PEC improved the productivity per cellin vitro. Each chromatograph-fraction of ascites was assayed for the enhancing activity.     

Foaming and enzyme activity in fungal cultures grown on sugar beet cosette

Summary Enzyme synthesis, foaming behaviour and its effects were studied using two common cellulolytic fungi;Trichoderma reesei andSporotrichum pulverulentum in a medium containing sugar beet cosette as a cellulosic substrate. Cellulase enzyme activities in the culture broth were found to be higher than the enzyme activities in natural and experimentally forced foam layers.