Genomic instability and mobile genetic elements in regions surrounding two discoidin I genes of Dictyostelium discoideum.

We have found that the genomic regions surrounding the linked discoidin I genes of various Dictyostelium discoideum strains have undergone rapid changes. Wild-type strain NC-4 has three complete discoidin I genes; its axenic derivative strain Ax-3L has duplicated a region starting approximately 1 kilobase upstream from the two linked genes and extending for at least 8 kilobases past the genes. A separately maintained stock, strain Ax-3K, does not have this duplication but has undergone a different rearrangement approximately 3 kilobases farther upstream. We show that there are repeat elements in these rapidly changing regions. At least two of these elements, Tdd-2 and Tdd-3, have characteristics associated with mobile genetic elements. The Tdd-3 element is found in different locations in related strains and causes a 9- to 10-base-pair duplication of the target site DNA. The Tdd-2 and Tdd-3 elements do not cross-hybridize, but they share a 22-base-pair homology near one end. At two separate sites, the Tdd-3 element has transposed into the Tdd-2 element, directly adjacent to the 22-base-pair homology. The Tdd-3 element may use this 22-base-pair region as a preferential site of insertion.

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Disruption of the RAD52 gene alters the spectrum of spontaneous SUP4-o mutations in Saccharomyces cerevisiae.

Genetics ◽

10.1093/genetics/122.3.535 ◽

1989 ◽

Vol 122 (3) ◽

pp. 535-542 ◽

Cited By ~ 1

Author(s):

B A Kunz ◽

M G Peters ◽

S E Kohalmi ◽

J D Armstrong ◽

M Glattke ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Base Pair ◽

Type Strain ◽

Wild Type Strain ◽

Wild Type ◽

Yeast Saccharomyces Cerevisiae ◽

Mutator Phenotype ◽

In The Wild ◽

Single Base Pair ◽

Almost All

Abstract Defects in the RAD52 gene of the yeast Saccharomyces cerevisiae confer a mutator phenotype. To characterize this effect in detail, a collection of 238 spontaneous SUP4-o mutations arising in a strain having a disrupted RAD52 gene was analyzed by DNA sequencing. The resulting mutational spectrum was compared to that derived from an examination of 222 spontaneous mutations selected in a nearisogenic wild-type (RAD52) strain. This comparison revealed that the mutator phenotype was associated with an increase in the frequency of base-pair substitutions. All possible types of substitution were detected but there was a reduction in the relative fraction of A.T----G.C transitions and an increase in the proportion of G.C----C.G transversions. These changes were sufficient to cause a twofold greater preference for substitutions at G.C sites in the rad52 strain despite a decrease in the fraction of G.C----T.A transversions. There were also considerable differences between the distributions of substitutions within the SUP4-o gene. Base-pair changes occurred at fewer sites in the rad52 strain but the mutated sites included several that were not detected in the RAD52 background. Only two of the four sites that were mutated most frequently in the rad52 strain were also prominent in the wild-type strain and mutation frequencies at almost all sites common to both strains were greater for the rad52 derivative. Although single base-pair deletions occurred in the two strains with similar frequencies, several classes of mutation that were recovered in the wild-type background including multiple base-pair deletions, insertions of the yeast transposable element Ty, and more complex changes, were not detected in the rad52 strain.(ABSTRACT TRUNCATED AT 250 WORDS)

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Action of a slowly hydrolysable cyclic AMP analogue on developing cells of Dictyostelium discoideum

Journal of Cell Science ◽

10.1242/jcs.35.1.321 ◽

1979 ◽

Vol 35 (1) ◽

pp. 321-338

Author(s):

C. Rossier ◽

G. Gerisch ◽

D. Malchow

Keyword(s):

Cyclic Amp ◽

Dictyostelium Discoideum ◽

Type Strain ◽

Wild Type Strain ◽

Agar Plate ◽

Cell Aggregation ◽

Fruiting Bodies ◽

Wild Type ◽

Camp Analogue ◽

Order Of Magnitude

Adenosine 3′,5′-cyclic phosphorothioate (cAMP-S) is a cyclic AMP (cAMP) analogue which is only slowly hydrolysed by phosphodiesterases of Dictyostelium discoideum. The affinity of cAMP-S to cAMP receptors at the cell surface is only one order of magnitude lower than that of cAMP. cAMP-S can replace cAMP as a stimulant with respect to all receptor-mediated responses tested, including chemotaxis and the induction of cAMP pulses. cAMP-S does not affect growth of D. discoideum but it blocks cell aggregation at a uniform concentration of 5 × 10(−7) M in agar plate cultures of strain NC-4 as well as its axenically growing derivative, Ax-2. Another wild-type strain of D. discoideum, v-12, is able to aggregate on agar plates supplemented with 1 mM cAMP-S. The development of Polysphondylium pallidum and P. violaceum is also highly cAMP-S resistant. In Ax-2 both differentiation from the growth phase to the aggregation-competent stage and chemotaxis are cAMP-S sensitive, whereas in v-12 only chemotaxis is inhibited. v-12 can still form streams of cohering cells and fruiting bodies when chemotaxis is inhibited by cAMP-S. Whereas cAMP induces differentiation into stalk cells at concentrations of 10(−3) or 10(−4) M, cAMP-S has the same effect in strain v-12 at the much lower concentration of 10(−6) M.

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NEW LOCI IN DICTYOSTELIUM DISCOIDEUM DETERMINING PIGMENT FORMATION AND GROWTH ON BACILLUS SUBTILIS

Genetics ◽

10.1093/genetics/96.1.115 ◽

1980 ◽

Vol 96 (1) ◽

pp. 115-123

Author(s):

James H Morrissey ◽

Steven Wheeler ◽

William F Loomis

Keyword(s):

Bacillus Subtilis ◽

Dictyostelium Discoideum ◽

Type Strain ◽

Wild Type Strain ◽

Wild Type ◽

Linkage Groups ◽

New Mutation ◽

Pigment Formation ◽

Complementation Groups ◽

First Time

ABSTRACT Seventeen independently isolated pigmentless (white) mutations in Dictyostelium discoideum are all recessive and fall into three complementation groups identifying two new whi loci in addition to the previously characterized whiA locus. whiB and whiC map to linkage groups III and IV, respectively. In addition, it was discovered that our laboratory stock of NC4, the wild-type strain from which these mutants were derived, has spontaneously lost the ability to grow on Bacillus subtilis. This new mutation, bsgB500, maps to linkage group VII and is not allelic to bsgA. bsgB500 is the first spontaneously derived mutation in D. discoideum that can be used to select heterozygous diploids, and for the first time allows genetic analysis to be routinely performed on strains derived from an unmutagenized background.

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The age-dependent loss of cells from the rear of a Dictyostelium discoideum slug is not tip controlled

Development ◽

10.1242/dev.61.1.61 ◽

1981 ◽

Vol 61 (1) ◽

pp. 61-67

Author(s):

Elizabeth Smith ◽

Keith L. Williams

Keyword(s):

Dictyostelium Discoideum ◽

Type Strain ◽

Wild Type Strain ◽

Organizer Region ◽

Cell Loss ◽

Wild Type ◽

Reciprocal Transplants ◽

Age Dependent ◽

Dependent Cell ◽

Cellular Slime

Young slugs of the cellular slime mould Dictyostelium discoideum drop small numbers of individual amoebae (∼ 10/mm) in the slime trail. With increased time of migration, slugs develop trailing tails and leave clumps of cells in their slime trails. Using reciprocal transplants between tips of young and old slugs and between a wild-type strain and an ‘aged'’ mutant it was shown that this age-dependent cell loss is due to changes in the bulk of cells comprising the slug, rather than to changes in the effectiveness of the tip (organizer region). Another property of the slug, the decision to continue migrating or form a fruiting body which is controlled by the tip, was less affected by age. This raises the possibility that cell autonomous properties of the slug are more subject to ageing than is the tip.

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Movement of the multicellular slug stage of Dictyostelium discoideum: an analytical approach

Development ◽

10.1242/dev.101.2.313 ◽

1987 ◽

Vol 101 (2) ◽

pp. 313-321 ◽

Cited By ~ 1

Author(s):

E.J. Breen ◽

P.H. Vardy ◽

K.L. Williams

Keyword(s):

Dictyostelium Discoideum ◽

Type Strain ◽

Analytical Approach ◽

Wild Type Strain ◽

Time Lapse ◽

Wild Type ◽

Forward Movement ◽

Migration Rates ◽

Video Recordings ◽

In The Wild

Time-lapse video recordings of migrating multicellular slugs of Dictyostelium discoideum were subjected to image analysis. A transient ‘collar-like’ structure was identified at the anterior end of the slug. This collar remains stationary in the wild- type strain WS380B; it is observed shortly after the advancing tip contacts the substratum. Stationary collars formed approximately every 12min; they were matched with patterns revealed on the underside of slime trails with FITC-coupled monoclonal antibody MUD50. It is proposed that stationary collars are involved with the forward movement of the slug. The mutant strain HU2421 lacks the MUD50-epitope and forms collars which do not remain stationary but move backwards along the slug to collect at a ‘waist’ region. The slipping-collars observed in the mutant correlated with very slow migration rates. We propose that HU2421 moves slowly because it lacks traction.

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Genetic dominance governs the evolution and spread of mobile genetic elements in bacteria

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2001240117 ◽

2020 ◽

Vol 117 (27) ◽

pp. 15755-15762

Author(s):

Jerónimo Rodríguez-Beltrán ◽

Vidar Sørum ◽

Macarena Toll-Riera ◽

Carmen de la Vega ◽

Rafael Peña-Miller ◽

...

Keyword(s):

Antibiotic Resistance ◽

Mobile Genetic Elements ◽

Model System ◽

Host Bacterium ◽

Wild Type ◽

Bacterial Evolution ◽

Human Interest ◽

Genetic Dominance ◽

Genetic Elements

Mobile genetic elements (MGEs), such as plasmids, promote bacterial evolution through horizontal gene transfer (HGT). However, the rules governing the repertoire of traits encoded on MGEs remain unclear. In this study, we uncovered the central role of genetic dominance shaping genetic cargo in MGEs, using antibiotic resistance as a model system. MGEs are typically present in more than one copy per host bacterium, and as a consequence, genetic dominance favors the fixation of dominant mutations over recessive ones. In addition, genetic dominance also determines the phenotypic effects of horizontally acquired MGE-encoded genes, silencing recessive alleles if the recipient bacterium already carries a wild-type copy of the gene. The combination of these two effects governs the catalog of genes encoded on MGEs. Our results help to understand how MGEs evolve and spread, uncovering the neglected influence of genetic dominance on bacterial evolution. Moreover, our findings offer a framework to forecast the spread and evolvability of MGE-encoded genes, which encode traits of key human interest, such as virulence or antibiotic resistance.

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Discovery of multiple anti-CRISPRs uncovers anti-defense gene clustering in mobile genetic elements

10.1101/2020.05.22.110304 ◽

2020 ◽

Cited By ~ 2

Author(s):

Rafael Pinilla-Redondo ◽

Saadlee Shehreen ◽

Nicole D. Marino ◽

Robert D. Fagerlund ◽

Chris M. Brown ◽

...

Keyword(s):

Mobile Genetic Elements ◽

Gene Clustering ◽

Type I ◽

Defense Gene ◽

Genetic Elements ◽

Defense Systems ◽

Prokaryotic Genomes ◽

New Type ◽

Genomic Regions ◽

Potential Exploitation

AbstractMany prokaryotes employ CRISPR-Cas systems to combat invading mobile genetic elements (MGEs). In response, some MGEs have evolved Anti-CRISPR (Acr) proteins to bypass this immunity, yet the diversity, distribution and spectrum of activity of this immune evasion strategy remain largely unknown. Here, we uncover 11 new type I anti-CRISPR genes encoded on numerous chromosomal and extrachromosomal mobile genetic elements within Enterobacteriaceae and Pseudomonas. Candidate genes were identified adjacent to anti-CRISPR associated gene 5 (aca5) and assayed against a panel of six type I systems: I-F (Pseudomonas, Pectobacterium, and Serratia), I-E (Pseudomonas and Serratia), and I-C (Pseudomonas), revealing the type I-F and/or I-E acr genes and a new aca (aca9). We find that acr genes not only associate with other acr genes, but also with inhibitors of distinct bacterial defense systems. These genomic regions appear to be “anti-defense islands”, reminiscent of the clustered arrangement of “defense islands” in prokaryotic genomes. Our findings expand on the diversity of CRISPR-Cas inhibitors and reveal the potential exploitation of acr loci neighborhoods for identifying new anti-defense systems.

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Metabolism of the cellular slime mould Dictyostelium discoideum grown in axenic culture

Biochemical Journal ◽

10.1042/bj1190175 ◽

1970 ◽

Vol 119 (2) ◽

pp. 175-182 ◽

Cited By ~ 79

Author(s):

J. M. Ashworth ◽

D. J. Watts

Keyword(s):

Dictyostelium Discoideum ◽

Wild Type Strain ◽

Specific Activity ◽

Axenic Culture ◽

Acid Oxidation ◽

Wild Type ◽

Free Sugars ◽

Slime Mould ◽

Cellular Slime ◽

Carbohydrate Contents

1. The DNA, RNA, protein and carbohydrate contents of myxamoebae of Dictyostelium discoideum strain Ax-2 were measured after growth on bacteria or in various axenic media. 2. Myxamoebae grown in the different axenic media have similar DNA, RNA and protein contents, but there are marked differences in the contents of glycogen and free sugars. The DNA and protein contents of myxamoebae grown on bacteria are different from those in myxamoebae grown axenically. 3. Approximately half the DNA found in myxamoebae grown on bacteria is of bacterial rather than of slime-mould origin. 4. The specific activities of some enzymes (including UDP-glucose pyrophosphorylase) are higher in myxamoebae grown axenically than in myxamoebae grown on bacteria. Nevertheless the characteristic increase in the specific activity of UDP-glucose pyrophosphorylase occurring during differentiation of cells of the wild-type strain NC-4 is also found in cells grown axenically. 5. The rate of amino acid oxidation during axenic growth of the myxamoebae is decreased when the cells are supplied with glucose.

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Evidence that Noncoding RNA dutA Is a Multicopy Suppressor of Dictyostelium discoideum STAT Protein Dd-STATa

Eukaryotic Cell ◽

10.1128/ec.00035-07 ◽

2007 ◽

Vol 6 (6) ◽

pp. 1030-1040 ◽

Cited By ~ 13

Author(s):

Nao Shimada ◽

Takefumi Kawata

Keyword(s):

Dictyostelium Discoideum ◽

Type Strain ◽

Noncoding Rna ◽

Target Genes ◽

Wild Type Strain ◽

Expression Patterns ◽

Wild Type ◽

Multicopy Suppressor ◽

Phosphorylated Form ◽

Multicopy Suppressors

ABSTRACT Dd-STATa, a Dictyostelium discoideum homologue of metazoan STAT transcription factors, is necessary for culmination. We created a mutant strain with partial Dd-STATa activity and used it to screen for unlinked suppressor genes. We screened approximately 450,000 clones from a slug-stage cDNA library for their ability to rescue the culmination defect when overexpressed. There were 12 multicopy suppressors of Dd-STATa, of which 4 encoded segments of a known noncoding RNA, dutA. Expression of dutA is specific to the pstA zone, the region where Dd-STATa is activated. In suppressed strains the expression patterns of several putative Dd-STATa target genes become similar to the wild-type strain. In addition, the amount of the tyrosine-phosphorylated form of Dd-STATa is significantly increased in the suppressed strain. These results indicate that partial copies of dutA may act upstream of Dd-STATa to regulate tyrosine phosphorylation by an unknown mechanism.

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