Codon usage in the vertebrate hemoglobins and its implications

A study of codon usage in vertebrate hemoglobins revealed an evolutionary trend toward elevated numbers of CpG codon boundary pairs in mammalian hemoglobin alpha genes. Selection for CpG codon boundaries countering the generally observed CpG suppression is strongly suggested by these data. These observations parallel recently published experimental results that indicate that constitutive expression of the human alpha-globin gene appears to be determined by regulatory information encoded within the structural gene. The possibility is raised that, in the absence of selection, CpG decay can be used to date the evolutionary origin of a mammalian alpha pseudogene from its active alpha gene.      

Evolution of crystallins: expression of lens-specific proteins in the blind mammals mole (Talpa europaea) and mole rat (Spalax ehrenbergi)

The mole (Talpa europaea; Insectivora) and the mole rat (Spalax ehrenbergi; Rodentia) both have degenerated eyes as a convergent adaptation to subterranean life. The rudimentary eye lenses of these blind mammals no longer function in a visual process. The crystallin genes, which display a lens-specific expression pattern, were studied in these blind mammals and in related species with normal eyes by hybridizing their genomic DNAs with probes obtained from cDNA clones for alpha A-, alpha B-, and beta Bp-crystallins from calf and gamma 3- crystallin from the rat. For all crystallin genes examined, the hybridization signals of mole and mole rat genomic DNA were comparable, respectively, with those of shrew and of rat and mouse, normal-vision representatives of the orders Insectivora and Rodentia. The expression of the crystallins at the protein level was tested by using antiserum specific for alpha-crystallin in immunofluorescence reactions on lens sections of mole and mole rat eyes and by using antisera against the beta- and gamma-crystallins on sections of the mole eye. All antisera gave positive fluorescence reactions exclusively with lens tissue of these blind mammals, indicating that the crystallins are still normally expressed despite the fact that these lenses have had no function in a visual process in these mammals for at least many million years. These findings apparently imply that some unknown selective advantage has conserved the crystallin genes and their expression after the loss of normal function of the lenses.      

Generalized Transduction in the Phytopathogen Pseudomonas syringae

Bacteriophages isolated from culture supernatants of Pseudomonas syringae pv. syringae and from sewage transferred various chromosomal genes to P. syringae PS224. Linkage between arginine and tryptophan loci was demonstrated. The number of transductants recovered per milliliter was not altered appreciably by UV irradiation of selected phage isolates. In addition, the presence of the IncP2 plasmid R38 in a P. syringae PS224 arginine auxotroph did not increase the transduction frequency as it does in Pseudomonas aeruginosa. Increasing the multiplicity of infection of transducing phage Pssy15 from 1 to 10 resulted in up to a 10-fold increase in the number of transductants recovered, although the actual transductional frequency remained about the same. Treatment of transduction mixtures with DNase did not affect transductional frequency.     

An investigation of bidirectional translocation in the Phloem

Patterns of (14) CO(2) , assimilate movement in Vicia jaba plants having 7 nodes were studied. Bidirectional translocation occurred throughout most of the stem length when tracer was applied to leaves of various ages. To determine whether this bidirectional translocation occurs within single sieve tubes, a O.1 % solution of the fluorescent dye K-fluorescein was applied to a lightly scraped area on the stem in the middle of a young internode. After one hour the dye was present short distances above and below the treated area. Free-hand sections of the internode showed the dye to be localized in the traces of the larger leaves below tbe treated area and in the traces of the younger leaves above the treated area. The dye was never present in the same bundle both above and below the treated area, indicating that each bundle and sieve tube translocated the dye in only one direction. These results were confirmed using Phaseolus vulgaris, Vinca rosea, and Pelargonium hortum. A similar study in which petioles of young Ecballium elaterium leaves were treated showed that usually the phloem of one bundle translocated the dye in only one direction but in some cases the external phloem of the bicollateral bundles carried the dye toward the stem while the internal phloem carried the dye toward the blade. When longer time intervals were used in all these experiments, the dye sometimes appeared in the same phloem areas both above and below the treated area. This is explained by a lateral transfer of tracer within the phloem, either through secondary phloem or through bundle anastomoses at the nodes.     

SIEVE TUBES AND CALLOSE IN ELODEA LEAVES

Detachment and incubation of Elodea leaves promoted callose synthesis in all cells, especially in epidermal pits and in sieve tubes. Phloem was detected in the midrib by fluorescent staining of callose induced to form on sieve plates. In EM views of mature sieve elements nucleus and tonoplast were lacking, mictoplasm replaced cytoplasm, mitochondria were fewer in number, and large plastids contained crystalline inclusion bodies. Slime was present as compact aggregates and as individual fibrils in mictoplasm and sieve pores. Deposition of callose is considered in relation to the blockage concept of callose function.     

Translocation blockage by sieve plate callose

Summary Axial translocation in 2-week-old cotton plants was inhibited by heating 4 cm of intact hypocotyl for 15 min by means of a 40–45° water jacket. A 1-cm jacket did not retard translocation, and temperatures below 40° had no effect. Translocation continued to be inhibited for at least 3 hours following heat treatment. After 6 hours, rates were equal to or above normal. Maximum amounts of callose were deposited on sieve plates after the heat treatment, but callose was noticeably diminished within 6 hours after heating and reduced to virtually normal levels within 2 days. Growth measurements, plasmolytic tests, vital staining, and visual observations revealed no evidence of injury in plants heated at 45°. Pore constriction from increased amounts of callose on sieve plates appears to be an effect of heating. Increased resistance due to such constriction may be an important factor in blockage of basipetal phloem translocation.Work supported in part by National Science Foundation Grant GB-2941. This material is abstracted from a dissertation presented in 1967 by R. B. McNairn to the Graduate Division, University of California at Davis in partial fulfillment of the requirements for the Ph. D. degree.All temperatures in this paper are in degrees centigrade (°C)     

Deletion and insertion mutants of the multidrug transporter

The multidrug transporter is a 170,000-dalton membrane glycoprotein which confers multidrug resistance through its activity as an ATP-dependent efflux pump for hydrophobic, cytotoxic drugs. To determine the essential structural components of this complex membrane transporter we have altered an MDR1 cDNA in an expression vector by deletion and insertion mutations. The structure of the transporter deduced from its amino acid sequence suggests that it consists of two homologous, perhaps functionally autonomous, halves each with six transmembrane segments and a cytoplasmic ATP-binding domain. However, several carboxyl-terminal deletions, one involving 53 amino acids, the second removing 253 amino acids, and an internal deletion within the carboxyl-terminal half of the molecule, totally eliminate the ability of the mutant transporter to confer drug resistance. An internal deletion of the amino-terminal half, which removed residues 140-229, is also nonfunctional. Small carboxylterminal deletions of up to 23 amino acids leave a functional transporter, although the removal of 23 COOH-terminal amino acids reduces its ability to confer colchicine resistance. Insertions of 4 amino acids in a transmembrane domain, and in one of the two ATP-binding regions, have no effect on activity. These studies define some of the limits of allowable deletions and insertions in the MDR1 gene, and demonstrate the requirement for two intact halves of the molecule for a functional multidrug transporter.     

The evolutionary history of the amylase multigene family in Drosophila pseudoobscura

In Drosophila pseudoobscura, the amylase (Amy) multigene family is contained within a series of inversions, or gene arrangements, on the third chromosome. The Standard (ST), Santa Cruz (SC), and Tree Line (TL) inversions are central to the phylogeny of arrangements, and have clusters of other arrangements derived from them. The gene arrangements belonging to each of these three clusters have a characteristic number of Amy genes, ranging from three in ST to two in SC to one in TL. This distribution pattern can reflect a history of either duplications or deletions, although the data available in the past did not permit a decision between these alternatives. We provide unambiguous evidence that three Amy genes were present before the divergence of the ST, SC, and TL arrangements. Thus, the current status of the Amy multigene family is the result of deletions in the TL and SC arrangements, which created three new pseudogenes: TL Amy2-psi, TL Amy3-psi, and SC Amy3- psi. Analysis of pseudogene sequences revealed that, in the SC and ST arrangements, pseudogene evolution has been retarded, most likely due to the homogenization effect of gene conversion. Finally, by determining the original copy number, we have reconstructed the evolutionary history of the Amy multigene family and linked it with the evolution of the central gene arrangements.      

Evidence for gene conversion in the amylase multigene family of Drosophila pseudoobscura

The alpha-amylase (Amy) multigene family in Drosophila pseudoobscura is located on the third chromosome, which is polymorphic for more than 40 inverted gene arrangements. The number of copies in this family ranges from one to three, depending on the arrangement in question. A previous study of the three Amy genes from the Standard (ST) arrangement suggested either that duplicated copies (Amy2 and Amy3) are functionally constrained or that they are undergoing gene conversion with Amy1. In order to elucidate further the pattern of molecular evolution in this family, we cloned and sequenced four additional Amy genes, two from the Santa Cruz (SC) and two from the Chiricahua (CH) gene arrangement. Of the two alternatives, only the hypothesis of gene conversion is supported by the sequence analysis. The homogenization effect of gene conversion has been strongest in SC, whose copies differ by only two nucleotides, less noticeable in ST, and negligible in the CH. Furthermore, the action of gene conversion is apparently localized, occurring only in the coding region. Interestingly, these results concur with the findings of other workers for the duplicated Amy genes in the Drosophila melanogaster group. Thus, the occurrence of gene conversion in the Amy multigene family seems to be a common feature in the Drosophila species studied so far.