Glenn A. Galau

Structural gene sets active in embryos and adult tissues of the sea urchin

Structural gene sequences active in a variety of sea urchin adult and embryo tissues are compared. A single-copy 3H-DNA fraction, termed mDNA, was isolated, which contains sequences complementary to the messenger RNA present on gastrula stage polysomes. Gastrula message sequences are 50 fold concentrated in the mDNA compared to total single-copy DNA. mDNA reactions were carried out with excess mRNA from blastula, pluteus, exogastrula, adult ovary, tubefoot, intestine, and coelomocytes, and with excess total mature oocyte RNA. A single-copy 3H-DNA fraction totally devoid of gastrula message sequences, termed null mDNA, was also reacted with these RNAs. Large differences in the extent of both mDNA and null mDNA reaction with the various RNAs were observed, indicating that in each state of differention a distinct set of structural genes is active, generally characterized by several thousand specific sequences. The complexity of gastrula mRNA was shown in previous work to be about 17 X 10(6) nucleotides. In units of 10(6) nucleotides, the complexities of the RNA sequence reacting with mDNA and with null mDNA in each tissue are, respectively, as follows: intestine mRNA: 2.1 and 3.7; coelomocyte mRNA: 3.5 and less than or equal to 1.4; tubefoot mRNA: 2.7 and less than or equal to 0.4; ovary mRNA: 13 and 6.7; oocyte total RNA: 17 and 20; blastula mRNA: 12 and 15; pluteus mRNA: 14 and less than or equal to 0.6; exogastrula mRNA: 14 and less than or equal to 0.6. The total complexity of each mRNA polulation is the sum of these values, as verified for several cases by reactions with total single-copy DNA. A relatively small set of mRNAs, the complexity of which is about 2.1 X 10(6) nucleotides, appears to be shared by several of the tissues studied.

A Measurement of the Sequence Complexity of Polysomal Messenger RNA in Sea Urchin Embryos

The first measurement has been made of the number of diverse mRNA sequences (mRNA sequence complexity) in the total polysomes of a eucaryotic system, the sea urchin gastrula. mRNA was purified of nuclear RNA and any other heterogeneous RNA contaminants by release from polysomes with puromycin. Trace quantities of labeled nonrepetitive DNA fragments were hybridized with an excess of mRNA. The hybridization reaction followed ideal first order kinetics in mRNA concentration. At completion of the hybridization reaction, 1.35% of the nonrepetitive DNA was present as mRNA-DNA hybrid. The hybridized DNA was extracted and was at least 70% hybridizable with mRNA, demonstrating a 50-fold purification of the expressed sequences. This purified DNA fraction reassociated with excess unfractionated sea urchin DNA at a rate identical to that of the total nonrepetitive DNA tracer. The mRNA had therefore been hybridized to nonrepetitive DNA sequence, and the amount of hybrid could be used as a direct measure of the mRNA sequence complexity. nThe complexity of the gastrula mRNA can be calculated as about 17 million nucleotides, sufficient to comprise some 14,000 distinct structural genes. This result also provides an estimate of the number of diverse proteins being translated in the gastrula. From the rate of mRNA-DNA hybrid formation, we estimate that about 8% of the mRNA belongs to this complex class, and that less than 500 copies of each species of message in this class exist per embryo. Most of the mRNA population consists of a relatively small number of diverse species represented a much larger number of times.

Comparative aspects of DNA organization in metazoa

Data on sequence organization in metazoa are reviewed and tabulated. It is shown that the features of sequence organization previously observed in Xenopus DNA are extremely widespread. At least 70% of DNA fragments 2,000–3,000 nucleotides long contain both single copy and repetitive sequence in all the organisms examined except Drosophila.

DNA sequence organization in the genomes of five marine invertebrates

The arrangement of repetitive and non-repetitive sequence was studied in the genomic DNA of the oyster (Crassostrea virginica), the surf clam (Spisula solidissima), the horseshoe crab (Limulus polyphemus), a nemertean worm (Cerebratulus lacteus) and a jellyfish (Aurelia aurita). Except for the jellyfish these animals belong to the protostomial branch of animal evolution, for which little information regarding DNA sequence organization has previously been available. The reassociation kinetics of short (250–300 nucleotide) and long (2,000–3,000 nucleotide) DNA fragments was studied by the hydroxyapatite method. It was shown that in each case a major fraction of the DNA consists of single copy sequences less than about 3,000 nucleotides in length, interspersed with short repetitive sequences. The lengths of the repetitive sequences were estimated by optical hyperchromicity and S1 nuclease measurements made on renaturation products. All the genomes studied include a prominent fraction of interspersed repetitive sequences about 300 nucleotides in length, as well as longer repetitive sequence regions.

Synthesis and turnover of polysomal mRNAs in sea urchin embryos

The synthesis and turnover kinetics of polysomal mRNA have been measured in sea urchin embryos. Polysomes were isolated from stages ranging between mesenchyme blastula and late gastrula Strongylocentrotus purpuratus embryos which had been exposed to exogenous 3H-guanosine. The amount of radioactivity incorporated into messenger and ribosomal RNAs was determined separately as a function of time, and the precursor pool specific activity was measured in the same embryos. Synthesis and decay rate constants were extracted from the data by a least-squares procedure. Per embryo, the rate of mRNA synthesis was calculated to be about 0.13 pg min-1, while the rate of rRNA synthesis is about 0.022 pg min-1. The newly synthesized mRNA turns over with a half-time of 5.7 hr. The data support only a single decay rate for the mRNA, but small fractions of mRNA decaying at different rates cannot be excluded. Previous studies have shown that a minor fraction of the mRNA includes the least abundant, most highly diverse set of messages (complex class mRNAs). To determine whether mRNAs of the complex class are synthesized and degraded at similar rates, labeled mRNA was measured in hybrids formed in mRNA excess reactions with single copy DNA. These experiments showed that complex class mRNAs represent an approximately proportional amount of the new mRNA symthesis, and turn over at the same average rate as does the bulk of the mRNA. Most of the mRNAs in the embryo polysomes are newly synthesized, rather than maternal. This statement refers both to complex class mRNAs and to prevalent mRNAs. Considering the sequence homology between embryo and oocyte mRNAs shown earlier, these results indicate that many of the same structural genes active during oogenesis are being transcribed in embryos at these stages.

Significance of rare mRNA sequences in liver

From mRNA-DNA hybridization studies it is known that eukaryotic mRNAs occur in several abundance classes. One such study with mammalian liver mRNA indicates that in this tissue the most complex abundance class consists of messenger RNAs present in 5–40 copies per cell. The other abundance classes are less complex and consist of mRNA sequences present an average of 250 and 7200 times per cell. In this paper we summarize approximate calculations of the number of mRNA molecules needed to sustain the steady-state quantities of 40 rodent liver proteins. Data were obtained from the literature regarding subunit molecular weights, degradation rate constants, and the concentration of each of these proteins in liver. The sample of proteins was chosen simply on the basis of the availability of the relevant data in the literature. For 13 of these proteins more direct estimates of mRNA frequency per cell could also be derived from measurements of the fraction of total protein synthesis accounted for by the protein in question. In all cases these estimates agreed within a factor of 2 to 3 with the values calculated from protein concentration and turnover rates. Several proteins known to be expressed in a histospecific way in liver were found to require steady-state mRNA concentrations in the range of only 1–30 copies per cell. This suggests that at least some of the mRNAs in the lowest abundance class are present as the result of the specific regulation of structural gene transcription.