Mutants of the Killer Plasmid of SACCHAROMYCES CEREVISIAE Dependent on Chromosomal Diploidy for Expression and Maintenance

Mutants of the killer plasmid of Saccharomyecs cerevisiae have been isolated that depend upon chromosomal diploidy for the expression of plasmid functions and for replication or maintenance of the plasmid itself. These mutants are not defective in any chromosomal gene needed for expression or replication of the killer plasmid.—Haploids carrying these mutant plasmids (called d for diploid-dependent) are either unable to kill or unable to resist being killed or both and show frequent loss of the plasmid. The wild-type phenotype (K⁺R⁺) is restored by mating the d plasmid-carrying strain with either (a) a wild-type sensitive strain which apparently has no killer plasmid; (b) a strain which has been cured of the killer plasmid by growth at elevated temperature; (c) a strain which has been cured of the plasmid by growth in the presence of cycloheximide; (d) a strain which has lost the plasmid because it carries a mutation in a chromosomal mak gene; or (e) a strain of the opposite mating type which carries the same d plasmid and has the same defective phenotype, indicating that the restoration of the normal phenotype is not due to recombination between plasmid genomes or complementation of plasmid or chromosomal genes.—Sporulation of the phenotypically K⁺R⁺ diploids formed in matings between d and wild-type nonkiller strains yields tetrads, all four of whose haploid spores are defective for killing or resistance or maintenance of the plasmid or a combination of these. Every defective phenotype may be found among the segregants of a single diploid clone carrying a d plasmid. These defective segregants resume the normal killer phenotype in the diploids formed when a second round of mating is performed, and the segregants from a second round of meiosis and sporulation are again defective.     

Defective Interference in the Killer System of Saccharomyces cerevisiae

The K₁ killer virus (or plasmid) of Saccharomyces cerevisiae is a noninfectious double-stranded RNA genome found intracellularly packaged in an icosahedral capsid. This genome codes for a protein toxin and for resistance to that toxin. Defective interfering virus mutants are deletion derivatives of the killer virus double-stranded RNA genome; such mutants are called suppressive. Unlike strains carrying the wild-type genome, strains with these deletion derivatives are neither toxin producers nor toxin resistant. If both the suppressive and the wildtype virus are introduced into the same cell, most progeny become toxin-sensitive nonkillers (J. M. Somers, Genetics 74:571-579, 1973). Diploids formed by the mating of a killer with a suppressive strain were grown in liquid culture, and RNA was extracted from samples taken up to 41 generations after the mating. The ratio of killer RNA to suppressive RNA decreased with increasing generations; by 41 generations the killer RNA was barely detectable. The copy numbers of the suppressive genome and its parental killer were virtually the same in isogenic strains, as were the growth rates of diploid strains containing either virus alone. Therefore, suppressiveness, not being due to segregation or overgrowth by faster growing segregants, is likely due to preferential replication or maintenance of the suppressive genome. Three suppressive viruses, all derivatives of the same killer virus (T. K. Sweeney et al., Genetics 84:27-42, 1976), did not coexist stably. The evidence strongly indicates that the largest genome of the three slowly suppressed both of the smaller genomes, showing that larger genomes can suppress smaller ones and that suppression can occur between two suppressives. Of 48 isolates of strains carrying the suppressive viruses, 5 had newly detectable RNA species, all larger than the original suppressive genomes. At least seven genes necessary for maintenance of the wild-type killer virus (MAK genes) were needed by a suppressive mutant. No effect of ski mutations (affecting regulation of killer virus double-stranded RNA replication) on suppressiveness was observed.     

Natural killer cell intrinsic toll-like receptor MyD88 signaling contributes to IL-12-dependent IFN-γ production by mice during infection with Toxoplasma gondii

Myeloid differentiation factor 88 (MyD88)-dependent IL-12 secretion by dendritic cells is critical for natural killer cell-mediated IFN-γ production and innate resistance to Toxoplasma gondii. Although MyD88^−/− mice challenged with T. gondii have defective IL-12 responses and succumb to infection, administration of IL-12 to MyD88^−/− mice fails to prevent acute mortality, suggesting that MyD88 may mediate signals within natural killer cells important for IL-12-dependent IFN-γ production and innate resistance to this parasite. In this study, we found that T. gondii antigens and IL-12 could synergistically trigger IFN-γ secretion by natural killer cells, which was dependent on toll-like receptor-MyD88 signaling. Further analysis showed that p38 mitogen-activated protein kinase, extracellular signal-regulated kinase, c-Jun N-terminal kinase and NF-κB multiple pathways downstream of MyD88 contributed to IFN-γ production by natural killer cells. Moreover, the well-established toll-like receptor agonists, T. gondii profilin (Tgprofilin) and T. gondii heat shock protein 70 (TgHSP70) could evoke a similar IFN-γ secretory response in natural killer cells to that evoked by T. gondii antigens. In vivo adoptive transfer experiments showed that, upon challenge with T. gondii, NOD/SCID-β2 microglobulin null (NOD/SCID-β2m^−/−) mice injected i.v. with MyD88^−/− natural killer cells had reduced serum IFN-γ levels and increased splenic tachyzoite burdens compared with those injected i.v. with wild-type natural killer cells. Taken together, these findings demonstrate a critical role for natural killer cell intrinsic toll-like receptor-MyD88 signaling in IL-12-dependent early IFN-γ production and innate resistance to T. gondii.     

Killer Phenomenon in USTILAGO MAYDIS: The Organization of the Viral Genome

The double-stranded RNA content, the production of inactive killer protein, and the presence of virus-like particles were examined in induced nonkiller mutants and nonkiller progeny from a cross between a killer strain and a sensitive strain. A correlation between the loss of the 0.7 x 10⁶ daltons dsRNA of the Ustilago maydis P6 virus and the lack of synthesis of the killer protein was established. In vitro and in vivo complementation between nonkiller strains provide additional support for the suggestion that the 0.7 x 10⁶ daltons dsRNA is related to the killer function. The coding capacity of the various species of dsRNA is discussed in relation to their possible function.     

Two Chromosomal Genes Required for Killing Expression in Killer Strains of SACCHAROMYCES CEREVISIAE

The killer character of yeast is determined by a 1.4 x 10⁶ molecular weight double-stranded RNA plasmid and at least 12 chromosomal genes. Wild-type strains of yeast that carry this plasmid (killers) secrete a toxin which is lethal only to strains not carrying this plasmid (sensitives). ——— We have isolated 28 independent recessive chromosomal mutants of a killer strain that have lost the ability to secrete an active toxin but remain resistant to the effects of the toxin and continue to carry the complete cytoplasmic killer genome. These mutants define two complementation groups, kex1 and kex2. Kex1 is located on chromosome VII between ade5 and lys5. Kex2 is located on chromosome XIV, but it does not show meiotic linkage to any gene previously located on this chromosome. ——— When the killer plasmid of kex1 or kex2 strains is eliminated by curing with heat or cycloheximide, the strains become sensitive to killing. The mutant phenotype reappears among the meiotic segregants in a cross with a normal killer. Thus, the kex phenotype does not require an alteration of the killer plasmid. ——— Kex1 and kex2 strains each contain near-normal levels of the 1.4 x 10⁶ molecular weight double-stranded RNA, whose presence is correlated with the presence of the killer genome.     

Genetic structure and regulation of a replicon of plasmid lambdadv.

Strains of Saccharomyces cerevisiae carrying a small double-stranded RNA species (the killer plasmid) secrete a toxin which is lethal only to strains not carrying this plasmid.We have isolated mutants in eight chromosomal genes essential for replication or maintenance of the killer plasmid, called mak1 through mak8. Seven of these genes have been mapped. mak4 and mak5 are on chromosome II; mak1 and mak8 are on chromosome XV; mak3 and mak6 are on chromosome XVI; and mak7 is on chromosome VIII. We have not yet located mak2. Two other chromosomal genes, m and pets, have been shown to be required for replication or maintenance of the killer plasmid.One allele of mak1 results in temperature sensitivity for host growth. Two independent pets isolates also result in the petite phenotype, as well as temperature sensitivity for growth.Wild-type killer strains have been reported to carry two species of doublestranded RNA of 2.5 × 10⁶ and 1.4 × 10⁶ molecular weight (designated L and M, respectively); wild-type non-killers carried only L. We estimate the size of the L and M species at 3.0 × 10⁶ and 1.7 × 10⁶ daltons, respectively. We have also detected a third species of double-stranded RNA of molecular weight 3.8 × 10⁶ (XL) present in all killer and non-killer strains examined.Mutation of any of mak1 through mak8 results in loss of the killer-associated species of double-stranded RNA (M; 1.7 × 10⁶). These mutants retain both the L species (3.0 × 10⁶) and the XL species (3.8 × 10⁶) of double-stranded RNA, and have acquired two new minor RNA species.     

Cytogenetic behavior of spore killer genes in neurospora

Crosses heterozygous and homozygous for Sk-1, Sk-2 and Sk-3 were examined by light microscopy. All three Spore killers behave similarly. In heterozygous killer x sensitive crosses, meiosis and ascospore development are normal until after the second postmeiotic mitosis when four of the eight ascospores in each ascus stop developing and degenerate. The four surviving ascospores carry the killer. Death of sensitives thus occurs only after killer and sensitive alleles, Sk^K and Sk^S, have segregated into separate ascospores. Homozygous killer x killer crosses do not show such a pattern of degeneration. Either all ascospores are normal or, if some fail to mature, they do not resemble the degenerating sensitive ascospores in heterozygous asci.——With Sk-2, it was shown that Sk^S nuclei do not abort when both Sk^K and Sk^S are present in the same ascospore. Mutants affecting ascus development were used to obtain large ascospores enclosing both Sk^K and Sk^S meiotic products in a common cytoplasm. Sk^S nuclei do not then undergo the degeneration that would be seen if they were sequestered into separate ascospores, and viable Sk^S progeny are recovered in undiminished numbers when the mixed multinucleate large ascospores are germinated. In a four-spored mutant, where each ascospore encloses a single nucleus following meiosis, degeneration of Sk^S ascospores nevertheless occurs, even though the third nuclear division is omitted. Cycloheximide and temperature treatments do not affect the expression of Sk^K.     

Fasting Enhances TRAIL-Mediated Liver Natural Killer Cell Activity via HSP70 Upregulation

Acute starvation, which is frequently observed in clinical practice, sometimes augments the cytolytic activity of natural killer cells against neoplastic cells. In this study, we investigated the molecular mechanisms underlying the enhancement of natural killer cell function by fasting in mice. The total number of liver resident natural killer cells in a unit weight of liver tissue obtained from C57BL/6J mice did not change after a 3-day fast, while the proportions of tumor necrosis factor–related apoptosis-inducing ligand (TRAIL)⁺ and CD69⁺ natural killer cells were significantly elevated (n = 7, p <0.01), as determined by flow cytometric analysis. Furthermore, we found that TRAIL⁻ natural killer cells that were adoptively transferred into Rag-2^−/− γ chain^−/− mice could convert into TRAIL⁺ natural killer cells in fasted mice at a higher proportion than in fed mice. Liver natural killer cells also showed high TRAIL-mediated antitumor function in response to 3-day fasting. Since these fasted mice highly expressed heat shock protein 70 (n = 7, p <0.05) in liver tissues, as determined by western blot, the role of this protein in natural killer cell activation was investigated. Treatment of liver lymphocytes with 50 µg/mL of recombinant heat shock protein 70 led to the upregulation of both TRAIL and CD69 in liver natural killer cells (n = 6, p <0.05). In addition, HSP70 neutralization by intraperitoneally injecting an anti- heat shock protein 70 monoclonal antibody into mice prior to fasting led to the downregulation of TRAIL expression (n = 6, p <0.05). These findings indicate that acute fasting enhances TRAIL-mediated liver natural killer cell activity against neoplastic cells through upregulation of heat shock protein 70.     

Dominant chromosomal mutation bypassing chromosomal genes needed for killer RNA plasmid replication in yeast

Yeast strains carrying a double-stranded RNA plasmid of 1.4–1.7 x 10⁶ daltons encapsulated in virus-like particles secrete a toxin that kills strains lacking this plasmid. The plasmid requires at least 24 chromosomal genes (pets, and mak1 through mak23) for its replication or maintenance. We have detected dominant Mendelian mutations (called KRB1 for killer replication bypass) that bypass two chromosomal genes, mak7 and pets, normally needed for plasmid replication. Strains mutant in mak7 and carrying the bypass mutation (mak7–1 KRB1) are isolated as frequent K⁺R⁺ sectors of predominantly K^-R ^- segregants from crosses of mak7–1 with a wild-type killer. All KRB1 mutations isolated in this way are inherited as single dominant centromere-linked chromosomal changes. They define a new centromere. KRB1 is not a translational suppressor. KRB1 strains contain a genetically normal killer plasmid and ds RNA species approximately the same in size and amount as do wild-type killers. Bypass of both mak7 and pets by one mutation suggests that these two genes are functionally related.

Two properties of the inheritance of KRB1 indicate an unusually high reversion frequency: (1) Heat or cycloheximide (treatments known to cure strains of the wild-type killer plasmid) readily induce conversion of mak7–1 KRB1 strains from killers to nonkillers with concomitant disappearance of KRB1 as judged by further crosses, and (2) mating two strains of the type mak7–1 KRB1 with each other yields mostly 2 K⁺R⁺: 2 K^-R^- segregation, although the same KRB1 mutation and the same killer plasmid are present in both parents.

     

Exploring the diploid wheat ancestral A genome through sequence comparison at the high-molecular-weight glutenin locus region

The polyploid nature of hexaploid wheat (T. aestivum, AABBDD) often represents a great challenge in various aspects of research including genetic mapping, map-based cloning of important genes, and sequencing and accurately assembly of its genome. To explore the utility of ancestral diploid species of polyploid wheat, sequence variation of T. urartu (A^uA^u) was analyzed by comparing its 277-kb large genomic region carrying the important Glu-1 locus with the homologous regions from the A genomes of the diploid T. monococcum (A^mA^m), tetraploid T. turgidum (AABB), and hexaploid T. aestivum (AABBDD). Our results revealed that in addition to a high degree of the gene collinearity, nested retroelement structures were also considerably conserved among the A^u genome and the A genomes in polyploid wheats, suggesting that the majority of the repetitive sequences in the A genomes of polyploid wheats originated from the diploid A^u genome. The difference in the compared region between A^u and A is mainly caused by four differential TE insertion and two deletion events between these genomes. The estimated divergence time of A genomes calculated on nucleotide substitution rate in both shared TEs and collinear genes further supports the closer evolutionary relationship of A to A^u than to A^m. The structure conservation in the repetitive regions promoted us to develop repeat junction markers based on the A^u sequence for mapping the A genome in hexaploid wheat. Eighty percent of these repeat junction markers were successfully mapped to the corresponding region in hexaploid wheat, suggesting that T. urartu could serve as a useful resource for developing molecular markers for genetic and breeding studies in hexaploid wheat.     

Information theoretic perspective on genome clustering

Shannon’s information theoretic perspective of communication helps one to understand the storage and processing of information in one-dimensional sequences. An information theoretic analysis of 937 available completely sequenced prokaryotic genomes and 238 eukaryotic chromosomes is presented. Information content (Id) values were used to cluster these chromosomes. Chargaff’s second parity rule i.e compositional self-complementarity, an empirical fact is observed in all the genomes, except for the proteobacteria Candidatus Hodgkinia cicadicola. High information content, arising out of biased base composition in all the 14 chromosomes of Plasmodium falciparum is found among two other genomes of prokaryotes viz. Buchnera aphidicola str. Cc (Cinara cedri) and Candidatus Carsonella ruddii PV. Despite size and compositional variations, both prokaryotic and eukaryotic genomes do not deviate significantly from an equiprobable and random situation. Eukaryotic chromosomes of an organism tend to have similar informational restraints as seen when a simple distance based method is used to cluster them. In eukaryotes, in certain cases, Id values are also similar for the two arms (p and q arm) of the chromosomes. The results of this current study confirm that the information content can provide insights into the clustering of genomes and the evolution of messaging strategies of the genomes. An efficient and robust Perl CGI standalone tool is created based on this information theory algorithm for the analysis of the whole genomes and is made available at https://github.com/AlagurajVeluchamy/InformationTheory.     

Cluster J Mycobacteriophages: Intron Splicing in Capsid and Tail Genes

Bacteriophages isolated on Mycobacterium smegmatis mc²155 represent many distinct genomes sharing little or no DNA sequence similarity. The genomes are architecturally mosaic and are replete with genes of unknown function. A new group of genomes sharing substantial nucleotide sequences constitute Cluster J. The six mycobacteriophages forming Cluster J are morphologically members of the Siphoviridae, but have unusually long genomes ranging from 106.3 to 117 kbp. Reconstruction of the capsid by cryo-electron microscopy of mycobacteriophage BAKA reveals an icosahedral structure with a triangulation number of 13. All six phages are temperate and homoimmune, and prophage establishment involves integration into a tRNA-Leu gene not previously identified as a mycobacterial attB site for phage integration. The Cluster J genomes provide two examples of intron splicing within the virion structural genes, one in a major capsid subunit gene, and one in a tail gene. These genomes also contain numerous free-standing HNH homing endonuclease, and comparative analysis reveals how these could contribute to genome mosaicism. The unusual Cluster J genomes provide new insights into phage genome architecture, gene function, capsid structure, gene mobility, intron splicing, and evolution.     

Comparative genomics of Bradyrhizobium japonicum CPAC 15 and Bradyrhizobium diazoefficiens CPAC 7: elite model strains for understanding symbiotic performance with soybean

Background

The soybean-Bradyrhizobium symbiosis can be highly efficient in fixing nitrogen, but few genomic sequences of elite inoculant strains are available. Here we contribute with information on the genomes of two commercial strains that are broadly applied to soybean crops in the tropics. B. japonicum CPAC 15 (=SEMIA 5079) is outstanding in its saprophytic capacity and competitiveness, whereas B. diazoefficiens CPAC 7 (=SEMIA 5080) is known for its high efficiency in fixing nitrogen. Both are well adapted to tropical soils. The genomes of CPAC 15 and CPAC 7 were compared to each other and also to those of B. japonicum USDA 6^T and B. diazoefficiens USDA 110^T.

Results

Differences in genome size were found between species, with B. japonicum having larger genomes than B. diazoefficiens. Although most of the four genomes were syntenic, genome rearrangements within and between species were observed, including events in the symbiosis island. In addition to the symbiotic region, several genomic islands were identified. Altogether, these features must confer high genomic plasticity that might explain adaptation and differences in symbiotic performance. It was not possible to attribute known functions to half of the predicted genes. About 10% of the genomes was composed of exclusive genes of each strain, but up to 98% of them were of unknown function or coded for mobile genetic elements. In CPAC 15, more genes were associated with secondary metabolites, nutrient transport, iron-acquisition and IAA metabolism, potentially correlated with higher saprophytic capacity and competitiveness than seen with CPAC 7. In CPAC 7, more genes were related to the metabolism of amino acids and hydrogen uptake, potentially correlated with higher efficiency of nitrogen fixation than seen with CPAC 15.

Conclusions

Several differences and similarities detected between the two elite soybean-inoculant strains and between the two species of Bradyrhizobium provide new insights into adaptation to tropical soils, efficiency of N₂ fixation, nodulation and competitiveness.

Electronic supplementary material

The online version of this article (doi: 10.1186/1471-2164-15-420) contains supplementary material, which is available to authorized users.     

Spore killer, a chromosomal factor in neurospora that kills meiotic products not containing it

Three chromosomal factors called Spore killer (Sk) have been found in wild populations of Neurospora sitophila and N. intermedia. Sk resembles other examples of meiotic drive such as Segregation Distorter in Drosophila, Pollen killer in wheat, and Gamete eliminator in tomato. In crosses heterozygous for Sk, each ascus contains four viable black ascospores and four inviable, undersize, clear ascospores, with second-division segregations infrequent. The survivors contain the killer allele Sk^K, while unlinked markers segregate normally. Reciprocal crosses are identical. When crosses are homozygous for an allele of Sk, all eight ascospores are viable and black in most asci. (Many homozygous crosses have a background level of randomly occurring inviable spores; however, the pattern of 4 viable: 4 small clear ascospores is not found in any of the asci of Sk-homozygous crosses.)——Killer (Sk-1^K) and sensitive (Sk-1^S) alleles occur in about equal numbers among a worldwide sample of N. sitophila strains, following no geographic pattern. No killer allele has been found in N. crassa. Sk-2^K and Sk-3^K, found in N. intermedia, are rare. Most N. intermedia strains are Sk-2^S and Sk-3^S, but some are wholly or partially resistant to one or both of the killer alleles, while not themselves acting as killers. Sk-2^K and Sk-2^R are both specific in conferring resistance to Sk-2^K, but not to Sk-3^K. Likewise Sk-3^K and Sk-3^R are resistant specifically to Sk-3^K, but not to Sk-2^K. Resistance segregates as an allele of Sk^K.——Sk-2 and Sk-3 have been mapped near the centromere of linkage group III after introgression into N. crassa, where crossing over is normally 11% between the proximal III markers acr-2 and leu-1. But crossing over is absent in this region when either of the killer alleles is heterozygous (Sk-2^K x Sk-2^S, Sk-3^K x Sk-3^S and Sk-2^K x Sk-2^R have been examined).     

A Novel Construction of Genome Space with Biological Geometry

A genome space is a moduli space of genomes. In this space, each point corresponds to a genome. The natural distance between two points in the genome space reflects the biological distance between these two genomes. Currently, there is no method to represent genomes by a point in a space without losing biological information. Here, we propose a new graphical representation for DNA sequences. The breakthrough of the subject is that we can construct the moment vectors from DNA sequences using this new graphical method and prove that the correspondence between moment vectors and DNA sequences is one-to-one. Using these moment vectors, we have constructed a novel genome space as a subspace in R^N. It allows us to show that the SARS-CoV is most closely related to a coronavirus from the palm civet not from a bird as initially suspected, and the newly discovered human coronavirus HCoV-HKU1 is more closely related to SARS than to any other known member of group 2 coronavirus. Furthermore, we reconstructed the phylogenetic tree for 34 lentiviruses (including human immunodeficiency virus) based on their whole genome sequences. Our genome space will provide a new powerful tool for analyzing the classification of genomes and their phylogenetic relationships.     

Planctomycetes attached to algal surfaces: Insight into their genomes

Planctomycetes are bacteria with complex molecular and cellular biology. They have large genomes, some over 7 Mb, and complex life cycles that include motile cells and sessile cells. Some live on the complex biofilm of macroalgae. Factors governing their life in this environment were investigated at the genomic level. We analyzed the genomes of three planctomycetes isolated from algal surfaces. The genomes were 6.6 Mbp to 8.1 Mbp large. Genes for outer-membrane proteins, peptidoglycan and lipopolysaccharide biosynthesis were present. Rubripirellula obstinata LF1^T, Roseimaritima ulvae UC8^T and Mariniblastus fucicola FC18^T shared with Rhodopirellula baltica and R. rubra SWK7 unique proteins related to metal binding systems, phosphate metabolism, chemotaxis, and stress response. These functions may contribute to their ecological success in such a complex environment. Exceptionally huge proteins (6000 to 10,000 amino-acids) with extracellular, periplasmic or membrane-associated locations were found which may be involved in biofilm formation or cell adhesion.     

Inverse PCR-Based Method for Isolating Novel SINEs from Genome

Short interspersed elements (SINEs) are moderately repetitive DNA sequences in eukaryotic genomes. Although eukaryotic genomes contain numerous SINEs copy, it is very difficult and laborious to isolate and identify them by the reported methods. In this study, the inverse PCR was successfully applied to isolate SINEs from Opsariichthys bidens genome in Eastern Asian Cyprinid. A group of SINEs derived from tRNA^Ala molecular had been identified, which were named Opsar according to Opsariichthys. SINEs characteristics were exhibited in Opsar, which contained a tRNA^Ala-derived region at the 5′ end, a tRNA-unrelated region, and AT-rich region at the 3′ end. The tRNA-derived region of Opsar shared 76 % sequence similarity with tRNA^Ala gene. This result indicated that Opsar could derive from the inactive or pseudogene of tRNA^Ala. The reliability of method was tested by obtaining C-SINE, Ct-SINE, and M-SINEs from Ctenopharyngodon idellus, Megalobrama amblycephala, and Cyprinus carpio genomes. This method is simpler than the previously reported, which successfully omitted many steps, such as preparation of probes, construction of genomic libraries, and hybridization.     

Antibody-dependent cellular cytotoxicity in the guinea pig: The role of the Kurloff cell

In the guinea pig, the killer cell in in vitro ADCC assays, is found to be the Fc receptor-bearing Kurloff cell. This killer Kurloff cell is under hormonal control, estrogen treatment significantly increasing the Kurloff cell numbers in blood, spleen, and thymus, and markedly augmenting the lytic capacity of these lymphoid compartments. The cytotoxic killer lymphocyte, if present, appears to be a minor effector cell in guinea pig ADCC. Selective lymphocyte subpopulation and Kurloff-cell depletion procedures reveal that the killer Kurloff cell may also possess a variety of other membrane markers (T⁺, C3⁺, Ig⁺). The particular membrane profile of a cytotoxic Kurloff cell is determined by its lymphoid site of residence and the hormonal status of the animal.     

Genome sequence of B. amyloliquefaciens type strain DSM7(T) reveals differences to plant-associated B. amyloliquefaciens FZB42

The complete genome sequence of Bacillus amyloliquefaciens type strain DSM7^T is presented. A comparative analysis between the genome sequences of the plant associated strain FZB42 (Chen et al., 2007) with the genome of B. amyloliquefaciens DSM7^T revealed obvious differences in the variable part of the genomes, whilst the core genomes were found to be very similar. The strains FZB42 and DSM7^T have in common 3345 genes (CDS) in their core genomes; whilst 547 and 344 CDS were found to be unique in DSM7^T and FZB42, respectively. The core genome shared by both strains exhibited 97.89% identity on amino acid level. The number of genes representing the core genome of the strains FZB42, DSM7^T, and Bacillus subtilis DSM10^T was calculated as being 3098 and their identity was 92.25%. The 3,980,199 bp genome of DSM7^T contains numerous genomic islands (GI) detected by different methods. Many of them were located in vicinity of tRNA, glnA, and glmS gene copies. In contrast to FZB42, but similar to B. subtilis DSM10^T, the GI were enriched in prophage sequences and often harbored transposases, integrases and recombinases. Compared to FZB42, B. amyloliquefaciens DSM7^T possessed a reduced potential to non-ribosomally synthesize secondary metabolites with antibacterial and/or antifungal action. B. amyloliquefaciens DSM7^T did not produce the polyketides difficidin and macrolactin and was impaired in its ability to produce lipopeptides other than surfactin. Differences established within the variable part of the genomes, justify our proposal to discriminate the plant-associated ecotype represented by FZB42 from the group of type strain related B. amyloliquefaciens soil bacteria.