Controlling the size of organs and organisms

A key difference between yeast and metazoans is the need of the latter to regulate cell proliferation and growth to create organs (and organisms) of reproducible size and shape. Great progress has been made in understanding how growth, cell size and the cell cycle are controlled in metazoans. Recent work has shown that disruption of conserved components of the insulin and Tor kinase pathways can alter organ size, indicating that the normal functioning of these pathways is essential for organ size control. However, disruption of genes that regulate patterning and of genes that control cell adhesion and cell polarity has a much more dramatic effect on final organ size than does manipulation of the cell cycle or of basal growth control mechanisms. These data point to an 'organ-size checkpoint' that regulates cell division, cell growth and apoptosis. Recent data suggests that cell competition may play an important role in implementing the organ-size checkpoint.     

Microheterogeneity detected in circular dimer mitochondrial DNA.

Exhaustive EcoRI digests of circular dimer mitochondrial DNA (mtDNA) from mouse cell lines LD and LDTK- yield two major fragments whose average lengths are slightly smaller than the corresponding fragments of circular monomer mtDNA from mouse LA9 and LMTK- cells. A third fragment approximately 400 nucleotide pairs in length is frequently produced in less than molar yield. Exhaustive EcoRI digests of circular dimer mtDNA from human acute myelogenous leukemic leucocytes yield three major fragments. The presence of mtDNA resistant to cleavage as well as fragments of intermediate sizes indicatesmicroheterogeneity in the genomic positions of EcoRI recognition sequences in both mouse and human circular dimer mtDNA. Analysis of the distribution averages of circular contour lengths indicates microheterogeneity in the sizes of mouse LD and human mtDNAs. The denatured-renatured EcoRI fragments frequently contain a small loop(s) of single-strand DNA as would occur for deletion(s) or addition(s) of single-strand DNA as would occur for deletion(s) or addition(s) of nucleotide sequences in some of the circular dimer molecules.     

Single strand-containing replicating molecules of circular mitochondrial DNA

Mitochondrial DNAs (mtDNAs) from Chang rat solid hepatomas and Novikoff rat ascites hepatomas were examined in the electron microscope after preparation by the aqueous and by the formamide protein monolayer techniques. MtDNAs from both tumors were found to include double-forked circular molecules with a form and size suggesting they were replicative intermediates. These molecules were of two classes. In molecules of one class, all three segments were apparently totally double stranded. Molecules of the second class were distinguished by the fact that one of the segments spanning the region between the forks in which replication had occurred (the daughter segments) was either totally single stranded, or contained a single-stranded region associated with one of the forks. Daughter segments of both totally double-stranded and single strand-containing replicating molecules varied in length from about 3 to about 80% of the circular contour length of the molecule. Similar classes of replicating molecules were found in mtDNA from regenerating rat liver and chick embryos, indicating them to be normal intermediates in the replication of mtDNA All of the mtDNAs examined included partially single-stranded simple (nonforked) circular molecules. A possible scheme for the replication of mtDNA is presented, based on the different molecular forms observed     

Large circular mitochondrial DNA in Crithidia luciliae

A novel circular DNA, 11.3 μm in contour length, has been found in a pure kinetoplast DNA fraction of Crithidia luciliae. The mitochondrial nature of the kinetoplast and the absence of these large circular molecules in the nuclear fraction of DNA suggest that they constitute the mitochondrial genome of this species.     

Ribonucleotides in closed circular mitochondrial DNA from HeLa cells

Closed circular mitochondrial DNA from HeLa cells is sensitive to both alkali and ribonucleases. The kinetics of ring opening in alkali suggest at least two classes of molecules. One class undergoes rapid breakdown, ultimately to fragments smaller than unit length, in contrast to the second class, which is more resistant to alkaline cleavage and is converted in large part to unit length single strands. Ribonucleases A, T₁ and H relax the supercoiled molecules, indicating that the alkali susceptibility is due to the presence of ribonucleotides in the DNA. By comparison with the rate of hydrolysis of RNA, the alkali-resistant class of mitochondrial DNA molecules is estimated to contain approximately 3 ribonucleotides and the alkalisensitive class 10–18.     

Stereologic studies on mitochondrial configuration in different organs of the rat

Summary Mitochondria from different organs of the rat with configurations ultrastructurally resembling those of isolated mitochondria of known respiratory states have been subjected to Stereologic analysis. Mitochondria were examined from mossy fibers of the granular layer of the cerebellar cortex (condensed state), of the pericentral hepatocytes (orthodox state), and of heart muscle and parietal cells of the gastric fundus (transitional state). In order to study the relationship between mitochondrial compartments and the internal membrane a partition coefficient was introduced, which expresses the volume of the matrix (E_mm) and external compartment (E_ocm) respectively per unit surface area of internal mitochondrial membrane. The Stereologic parameters investigated, i.e. surface density of the mitochondrial membranes, volume density of the mitochondrial compartments and membranes, and partition coefficients generally agreed with the visual evaluation of mitochondrial ultrastructure. However, analysis of the coefficient of variation /x × 100% for E_ocm and E_mm has shown significantly greater variability in the mitochondria of the myocardium than in the gastric mitochondria, despite similar ultrastructure. It is suggested that Stereologic methods, like time-lapse cinematography, give a compound picture of configurational variation and of its plasticity.     

Analysis of four tobacco mitochondrial DNA size classes

Supercoiled mtDNAs were isolated from tobacco suspension culture cells and three of the smallest size classes (10.1, 20.2 and 30.3 kb) were characterized through denaturation, heteroduplex and restriction mapping. The 20.2 molecule was found to be a head-to-tail dimer of the 10.1 or X size class, while the 30.3 kb size class was found to contain two kinds of molecules, a head-to-tail trimer of X (X3) and a second molecule, ABC. X and ABC had a 118 +/- 35 bp region of homology, and both size classes shared a degree of homology with at least one other size class. Restriction maps of both the X and ABC molecules are presented and the possible origin and role of the many plant mtDNA size classes are discussed.     

The mitochondrial DNA helicase TWINKLE can assemble on a closed circular template and support initiation of DNA synthesis

Mitochondrial DNA replication is performed by a simple machinery, containing the TWINKLE DNA helicase, a single-stranded DNA-binding protein, and the mitochondrial DNA polymerase γ. In addition, mitochondrial RNA polymerase is required for primer formation at the origins of DNA replication. TWINKLE adopts a hexameric ring-shaped structure that must load on the closed circular mtDNA genome. In other systems, a specialized helicase loader often facilitates helicase loading. We here demonstrate that TWINKLE can function without a specialized loader. We also show that the mitochondrial replication machinery can assemble on a closed circular DNA template and efficiently elongate a DNA primer in a manner that closely resembles initiation of mtDNA synthesis in vivo.     

5-bromodeoxyuridine labeling of monomeric and catenated circular mitochondrial DNA in HeLa cells

Bromouracil labeling of the mitochondrial DNA in exponentially growing HeLa cells produces two hybrid mitochondrial DNA species, with density shifts of 41.9 and 54.0 mg/ml relative to unlabeled mitochondrial DNA, as well as heavy mitochondrial DNA, with a shift of 95.3 mg/ml. The two hybrid species result from the difference in thymine composition of the complementary strands of mitochondrial DNA. In addition, mitochondrial DNA with a density intermediate between the hybrid and unlabeled species was found. This quarter heavy mitochondrial DNA represents 25% (w/w) of the total DNA after eight hours of labeling, and forms two peaks with shifts of 20.6 and 27.0 mg/ml relative to unlabeled mitochondrial DNA. 70% (w/w) of the quarter heavy mitochondrial DNA is in catenated forms, while 30% (w/w) is monomeric. Degradation of the catenanes by shearing of purified quarter heavy mitochondrial DNA results in the appearance of hybrid and unlabeled mitochondrial DNA bands, demonstrating that the quarter heavy catenanes contain both hybrid and unlabeled submolecules. The implications of the structure of the quarter heavy catenanes on the mechanism of formation of catenanes are discussed.     

Estimation of circular DNA size using gamma-irradiation and pulsed-field gel electrophoresis

A method is described for estimating the size of large circular DNAs found within complex chromosomal DNA preparations. DNAs are treated with low levels of gamma-irradiation, sufficient to introduce a single double-stranded break per circle, and the resulting linear DNA is sized by pulsed-field electrophoresis and blot hybridization. The method is fast, reproducible, and very conveniently applied to the agarose-enclosed chromosomal DNA preparations commonly used in pulsed field electrophoresis.     

The inhibition of systrophe in different organisms

Summary The phenomenon of systrophe following different stimuli was comparatively investigated in the cells of different plant organisms. In all cases systrophe could be inhibited by metabolic inhibitors. The influence of colchicine, cytochalasin B, vinblastine and APM (amiprophos-methyl) varied.     

The size of mitochondrial DNA from a cytoplasmic petite mutant of Saccharomyces cerevisiae

Summary Mitochondrial DNA has been isolated from a cytoplasmic petite mutant of Saccharomyces cerevisiae which has retained only about 2% of the mitochondrial wild type genome. The denatured DNA was analyzed by agarose gel electrophoresis and a homogeneous, single band of DNA was found. Petite and wild type mitochondrial DNAs exhibited similar gel electrophoretic mobilities. Using denatured DNA from the E. coli phages T4 and T3 for comparison a molecular weight of 55×10⁶ daltons has been calculated for the double-stranded petite mitochondrial DNA. On the basis of this observation most of the mitochondrial DNA of this petite mutant appeared to consist of a polymer of about 50 repeats to account for a size similar to that of the wild type molecule. Thus a regulatory mechanism might exist which keeps constant the physical size of the mitochondrial DNA molecule in spite of the elimination of large fractions of the wild type genome.Dedicated to Dr. Dr. h. c. Peter Michaelis on the occasion of his 75th birthday     

Characteristics of nucleotide blocks in coding and non-coding DNA sequences from different organisms

A statistical analysis of occurrence of particular nucleotide runs (1 divided by 10 nucleotides long) in DNA sequences of different species has been carried out. There are considerable differences in run distributions in DNA sequences of prokaryotes, invertebrates and vertebrates. Distribution of various types of runs has been found to be different in coding and non-coding sequences. There is an abundance of short runs 1 divided by 2 nucleotides long in coding sequences, and there is a deficiency of such runs in the non-coding regions. However, some interesting exceptions from this rule exist: for run distribution of adenine in prokaryotes and for distribution of purine-pyrimidine runs in eukaryotes. This may be stipulated by the fact that the distribution of runs are predetermined by structural peculiarities of the entire DNA molecule. Runs of guanine or cytosine of three to six nucleotides long occur predominantly in the non-coding DNA regions in eukaryotes, especially in vertebrates.     

N-Nitrosomorpholine induced alterations of unscheduled DNA synthesis, mitochondrial DNA synthesis and cell proliferation in different cell types of liver, kidney, and urogenital organs in the rat

In order to measure rates of unscheduled DNA synthesis (UDS), mitochondrial DNA synthesis, and cell proliferation, i.e. factors relevant in the early phase of carcinogenesis, young rats received by gavage 200 mg/kg N-nitrosomorpholine (NNM) or vehicle (distilled water), and were injected with 3H-thymidine 24 h later. Autoradiographs from liver, kidney, urethra, prostate, seminal vesicle, and ductus deferens were prepared from deparaffinized sections, using a 250-day exposure time. In the liver, UDS was at least doubled in 2n and 4n hepatocytes. Approximately 3% of these hepatocytes exhibited a fourfold increase in UDS. Such strongly labeled cells were only observed in the liver following NNM exposure. With the exception of renal epithelial cells of the proximal tubule, UDS in epithelial cells of bladder, urethra, ductus deferens, seminal vesicle and prostate was decreased in NNM-exposed rats. Mitochondrial DNA synthesis and cell proliferation were significantly increased only in hepatocytes, and were decreased in all other monitored organs in NNM-exposed rats. The strongly increased UDS and more moderately increased mitochondrial DNA synthesis in a subgroup of hepatocytes suggest that possibly some unrepaired damage persists in the DNA of these cells. The latter cells may be the precursors of so-called foci of hepatocellular alteration, which appear later during the process of carcinogenesis. The increased UDS but decreased rate of proliferation in the renal proximal tubule cells might be related to renal carcinogenesis which is observed in NNM-exposed rats after a long latency period.