The zoospore and meiospore of the aquatic phycomyceteCatenaria anguillulae

Summary The zoospore and meiospore of the aquatic phycomyceteCatenaria anguillulae (Phycomycetes, Blastocladiales, Catenariaceae) have a nuclear cap enclosing the cellular ribosomes within a double membrane, and a side body complex which is very similar to that observed in zoospores ofBlastocladiella andCoelomomyces and is structurally related to the side body complex observed in spores ofAllomyces. The structural organization of the side body complex and striated rootlet is analyzed from serial sections.The meiospore also contains an array of flattened cisternae which are in direct contact with, and appear to be derived from, the outer nuclear membrane and the backing membrane of the side body complex.The structural organization of the zoospore and meiospore ofC. anguillulae is compared to and contrasted with the structural organization observed in spores of members of theChytridiales, Blastocladiales, Monoblepharidales, andHarpochytriales. It is concluded that the structural organization of the spores of theBlastocladiales, Monoblepharidales, andHarpochytriales is similar, and affinities in spore organization can be found in some members of theChytridiales.     

Identification of a gene family (kat) encoding kinesin-like proteins in Arabidopsis thaliana and the characterization of secondary structure of KatA

A gene family, designated kat, has been characterized in Arabidopsis thaliana by genomic Southern hybridization and nucleotide sequencing analysis. The kat gene family includes at least five members, named katA, katB, katC, katD and katE, whose products share appreciable sequence similarities in their presumptive ATP-binding and microtubule-binding motifs with known kinesin-like proteins. The carboxyl-terminal region of the KatA protein deduced from the nucleotide sequence of the cDNA clone has considerable homology with the mechanochemical motor domain of the kinesin heavy chain. The predicted secondary structure of the KatA protein indicates two globular domains separated by a long a helical coiled coil with heptad repeat structures, such as are commonly found in kinesin-like proteins.     

A method for estimating rates of nucleotide substitution using DNA sequence data

An estimate of the average number of evolutionarily acceptable substitutions per nucleotide since the most recent common ancestor of a pair of homologous sequences is found which uses nucleotide sequence data. The estimate is derived assuming a Poisson-like model for the evolutionary process. A method is also suggested for analyzing nucleotide sequence data in M homologous sequences (M 3). A simulation study is reported showing that the estimates are satisfactory providing there is sufficient homology between the sequences. To demonstrate the methods a numerical example using some β-globin data is presented.     

Phylogenetic relationship withinFusarium sambucinum Fuckel sensu lato,determined from ribosomal RNA sequences

Partial ribosomal RNA nucleotide sequences were determined for 11 strains ofFusarium sambucinum Fuckelsensu lato to assess by molecular genetic means, Nirenberg's recent morphotaxonomic interpretation which split the species into three distinct taxa:F. sambucinum sensu stricto, F. torulosum, and one other species, as yet unnamed (Fusarium species nova). Four sequence patterns were identified among the 11 strains. Two sequences that varied at one site were found among strains ofF. sambucinum, strains ofF. torulosum andFusarium sp. nov. showed no intraspecific variation. Interspecific comparisons revealed nucleotide sequence differences of 3–9 substitutions in the ca. 240 nucleotide rRNA segment examined. Although interspecific differences are not large in terms of percent nucleotide substitution, they are much larger than the observed intraspecific variation and support the morphological interpretation distinguishing three taxa. When the data were analysed using parsimony and bootstrapping, the three taxon tree was well supported. The phylogenetic arrangement of these strains is congruent with secondary metabolite profile similarities.     

Deoxyribonucleic acid reassociation in the classification of coagulase-positive staphylococci

DNA-DNA reassociation studies were performed with coagulase-positive staphylococci belonging to the biotypes A, B, C, D, E and F. These studies present genetic evidence for the existence of at least two distinct species within this group of organisms. The common Staphylococcus aureus strains were represented by organisms from biotypes A to D, and their DNA revealed over 80% nucleotide sequence homology under restrictive conditions. Less than 15% DNA homology was detected between strains from biotypes A to D (S. aureus) and those from biotypes E and F. The DNA of organisms from either the biotypes E or F displayed over 70% homology. Together, both biotypes are considered to represent the species S. intermedius. However, DNA homology values dropped to 50–65% between strains from different biotypes. This may justify the separation of S. intermedius biotypes E and F on a subspecies level.Abbreviations O.D. optical density - SSC standard saline citrate buffer (0.15 M NaCl, 0.015 M sodium citrate, pH 7.0) This work was supported by Deutsche Forschungsgemeinschaft     

Lactic dehydrogenase activity and cellular localization of several dehydrogenases in Neurospora and Allomyces

Summary Lactic dehydrogenase (LDH) activity has been cytochemically localized and its activity measured in wild-type and mutant strains of Neurospora crassa and male and female hybrids of Allomyces.In all strains, less intracellular staining is found, by oxidative assay of lactic dehydrogenase, ethanol dehydrogenase and a few other dehydrogenases, in the hyphal tips than in the older regions of the hyphae.The extractible activity of LDH, assayed reductively in the soluble fraction, is much greater in Allomyces than Neurospora. In Allomyces the least activity is found in the female differentiated strain. The male differentiated strain and especially the vegetative cultures of both strains have much more activity. In Neurospora, conidiating cultures have unexpectedly more activity than vegetative cultures. The crisp mutant which forms increased numbers of conidia has more activity than the wild-type which, in turn, has more activity than the aconidial fluffy mutant.     

The Arabidopsis thaliana ATP-binding cassette proteins: an emerging superfamily

Solute transport systems are one of the major ways in which organisms interact with their environment. Typically, transport is catalysed by integral membrane proteins, of which one of the largest groups is the ATP‐binding cassette (ABC) proteins. On the basis of sequence similarities, a large family of ABC proteins has been identified in Arabidopsis. A total of 60 open reading frames (ORFs) encoding ABC proteins were identified by BLAST homology searching of the nuclear genome. These 60 putative proteins include 89 ABC domains. Based on the assignment of transmembrane domains (TMDs), at least 49 of the 60 proteins identified are ABC transporters. Of these 49 proteins, 28 are full‐length ABC transporters (eight of which have been described previously), and 21 are uncharacterized half‐transporters. Three of the remaining proteins identified appear to be soluble, lacking identifiable TMDs, and most likely have non‐transport functions. The eight other ORFs have homology to the nucleotide‐binding and transmembrane components of multi‐subunit permeases. The majority of ABC proteins found in Arabidopsis can, on the basis of sequence homology, be assigned to subfamilies equivalent to those found in the yeast genome. This assignment of the Arabidopsis ABC proteins into easily recognizable subfamilies (with distinguishable subclusters) is an important first step in the elucidation of their functional role in higher plants.     

Nucleotide sequence of the staphylococcal enterotoxin C1 gene and relatedness to other pyrogenic toxins

Summary The nucleotide sequence for the structural gene entC1 encoding staphylococcal enterotoxin C1 was determined. The gene contained 801 bp and coded for a protein of 266 amino acids. Of these, 27 comprised the signal peptide. Cleavage of the signal peptide resulted in a mature protein with 239 amino acids and a calculated molecular weight of 27496. The nucleotide sequence of entC1 shared considerable homology (74% and 59%, respectively) with genes encoding enterotoxin B and streptococcal pyrogenic exotoxin A. A similar degree of amino acid homology was observed after alignment of the respective proteins. Thus, certain regions of these three toxin molecules possess structural similarities that may be responsible for shared biological properties.     

Interspecific transformation and DNA characteristics in Allomyces

Summary Heterologous deoxyribonucleic acid treatment in Allomyces has been shown to transfer epigynous versus hypogynous character in the recipient species.A certain proportion of inverted sexual arrangements have been consistently detected in the acceptors.The uptake of native DNA was demonstrated using labelled ³²P-nucleic acid. The uptake was found to be higher in homologous (controls) than heterologous receptors.Chromatographic fractionation of the total DNA reveals 3 types differing in their Tm values and therefore GC ratios; these appear to be localized in nuclei, mitochondria and residual cytoplasm.     

Amounts and patterns of nucleotide variation within and between two Japanese conifers, sugi (Cryptomeria japonica) and hinoki (Chamaecyparis obtusa) (Cupressaceae sensu lato)

Sugi (Cryptomeria japonica) and hinoki (Chamaecyparis obtusa) are the most important timber species in Japan. To quantify and compare the level of nucleotide variation in these species, we investigated their variation at ten nuclear loci. Average values of nucleotide diversity at synonymous sites (π _SYN) found in sugi and hinoki were 0.0038 and 0.0069, respectively. However, although the average value of nucleotide diversity was higher in hinoki than in sugi, their average values of haplotype diversity were similar. Deviations from the standard neutral model were detected at two loci in hinoki using Tajima’s D, Fay and Wu’s H, and Strobeck’s S statistics, which seem to be due to its historical population structure. Levels of divergence between the two species at synonymous sites of the ten genes ranged from 0.121 to 0.566 (0.28 on average). These values positively correlated with their guanine + cytosine contents at third-codon positions of synonymous sites (%GC3s).     

Phylogenetic relationships among Fusarium species measured by DNA reassociation

Deoxyribonucleic acid of 11 Fusarium species (F. acuminatum, F. arthrosporioides, F. avenaceum, F. culmorum, F. graminearum, F. heterosporum, F. moniliforme, F. oxysporum, F. sambucinum, F. semitectum, F. solani) have been compared with respect to their physical characteristics (T_m, % G + C), homology values and nucleotide sequence divergence.A phylogenetic tree based on physical characteristics, homology values and differences in percentage divergence of Fusarium species DNAs has been constructed.     

STUDIES OF THE MOTILE CELLS OF CHYTRIDS. V. FLAGELLAR RETRACTION IN POSTERIORLY UNIFLAGELLATE FUNGI

Presented are observations of 17 species in the following 14 genera. Blastocladiales : Allomyces and Blastocladiella. Chytridiales : Asterophlyctis, Catenochytridium, Chytridium, Chytriomyces, Cladochytrium, Entophlyctis, Phlyctochytrium, Rhizophlyctis, Rozella, Septochytrium, and two undescribed cladochytriaceous genera. Encystment without flagellar retraction is briefly considered. Recognized and described are four basic developmental patterns or methods of flagellar retraction: lash-around, body-twist, straight-in, and vesicular. Variations in and combinations of the four basic methods are described. Observations, most of which are illustrated with brightfield, darkfield, phase-contrast, and electron microscopy, along with what is known from the literature, are discussed and serve as the basis for generalized, summary diagrams or two-dimensional models of patterns of flagellar retraction in posteriorly uniflagellate fungi. An endeavor is made to put the findings reported on in this paper in historical, morphogenetic, and phylogenetic perspective.     

Nucleotide sequence of the gene for Escherichia coli ribosomal protein S15 (rpsO)

Summary The nucleotide sequence of the ribosomal protein gene rpsO (S15) and its flanking region were determined. The amino acid sequence of S15 protein deduced from the nucleotide sequence is in good agreement with the published amino acid sequence with one exception. The nucleotide sequence shows two probable promoter sites about 100 nucleotides upstream from the initiation codon (AUG) of rpsO. Inspection of the sequence also revealed structural homology between the distal part of rpsO and the reported S15 binding region in 16S rRNA.     

Multiple copies of the insertion-DNA sequences IS1 and IS2 in the chromosome of E. coli K-12

Summary About 8 copies of the DNA sequence IS1 (which consists of 800 nucleotide pairs) and about 5 copies of the DNA sequence IS2 (1400 nucleotide pairs) have been detected by DNA-DNA hybridization in the chromosome of E. coli K-12. No homology is observed between IS1 and IS2. Both IS1 and IS2 are also found in the DNA of the F plasmid.     

The sequence-immunology correlation revisited: Data for cetacean myoglobins and mammalian lysozymes

Quantitative microcomplement fixation tests employing rabbit antisera were done to compare immunologically 13 cetacean myoglobins and 15 mammalian lysozymes c of known amino acid sequence. In both cases there was a strong correlation between immunological distance (y) and percent sequence difference (x), as had been found for several other globular proteins. For myoglobin the relationship could be described by y = 10.5x and for lysozyme by y = 8.5x. The coefficients in both of these equations are appreciably higher than the values of 5.1–6.9 reported for three other vertebrate globular proteins (bird lysozyme c, mammalian ribonuclease, and mammalian serum albumin), and they imply that rabbit antisera to mammalian myoglobins and lysozymes are more sensitive to evolutionary substitutions. A strong inverse correlation (r = -0.95) was found when the slope of the line relating y to x for these five data sets was plotted against the percent sequence difference between the rabbit's own protein and the proteins immunized with. Specifically, the cetacean myoglobins on average differ in amino acid sequence from rabbit myoglobin by less than 13% and exhibit the steepest slope (10.5), while bird lysozyme sequences differ by nearly 40% from rabbit lysozyme and exhibit the shallowest slope (5.1).     

Cloning and nucleotide sequence of an archaebacterial glutamine synthetase gene: Phylogenetic implications

Summary The glnA gene of the thermophilic sulphur-dependent archaebacterium Sulfolobus solfataricus was identified by hybridization with the corresponding gene of the cyanobacterium Spirulina platensis and cloned in Escherichia coli. The nucleotide sequence of the 1696 bp DNA fragment containing the structural gene for glutamine synthetase was determined, and the derived amino acid sequence (471 residues) was compared to the sequences of glutamine synthetases from eubacteria and eukaryotes. The homology between the archaebacterial and the eubacterial enzymes is higher (42%–49%) than that found with the eukaryotic counterpart (less than 20%). This was true also when the five most conserved regions, which it is possible to identify in both eubacterial and eukaryotic glutamine synthetases, were analysed.     

Molecular characterization of the rbcS multi-gene family of Petunia (Mitchell)

Summary The small subunit (RbcS) of ribulose bisphosphate carboxylase (RuBPCase) is encoded by eight genes in Petunia (Mitchell). These genes can be divided into three subfamilies (51, 117 and 71) based upon hybridization to three petunia rbcS cDNA clones. The nucleotide sequence of six of the eight petunia rbcS genes is presented here and the structure of the genes is discussed with respect to their genomic linkage and their expression levels in petunia leaf tissue. The rbcS genes belonging to the same subfamily encode an identical mature RbcS polypeptide, however the different subfamilies encode distinguishable polypeptides. All the genes, except one, contian two introns within the mature subunit coding region; one gene contains one extra intron within the coding region. There are large regions of nucleotide sequence homology within the introns of genes within a subfamily, but significantly less homology between the introns of genes of different subfamilies. A complex pattern of homology within the multiple genes of the 51 subfamily is observed. There are regions within these genes which share high levels of sequence homology; this homology does not extend throughout the whole gene and the regions of homology do not always occur in adjacent genes. Two 3 rbcS gene fragments which we isolated from the petunia genome show high levels of homology to two of the intact rbcS genes.     

The comparative amino acid sequences, substrate specificities and gene or cDNA nucleotide sequences of some prokaryote and eukaryote amidinotransferases: implications for evolution

The amino acid sequences of the amidinotransferases and the nucleotide sequences of their genes or cDNA from four Streptomyces species (seven genes) and from the kidneys of rat, pig, human and human pancreas were compared. The overall amino acid and nucleotide sequences of the prokaryotes and eukaryotes were very similar and further, three regions were identified that were highly identical. Evidence is presented that there is virtually zero chance that the overall and high identity regions of the amino acid sequence similarities and the overall nucleotide sequence similarities between Streptomyces and mammals represent random match. Both rat and lamprey amidinotransferases were able to use inosamine phosphate, the amidine group acceptor of Streptomyces. We have concluded that the structure and function of the amidinotransferases and their genes has been highly conserved through evolution from prokaryotes to eukaryotes. The evolution has occurred with: (1) a high degree of retention of nucleotide and amino acid sequences; (2) a high degree of retention of the primitive Streptomyces guanine+cytosine (G+C) third codon position composition in certain high identity regions of the eukaryote cDNA; (3) a decrease in the specificities for the amidine group acceptors; and (4) most of the mutations silent in the regions suggested to code for active sites in the enzymes.     

Assembly of colicin genes from a few DNA fragments. Nucleotide sequence of colicin D

The nucleotide sequence of a 2.4 kb Dral-EcoRV fragment of pColD-CA23 DNA was determined. The segment of DNA contained the colicin D structural gene (cda) and the colicin D immunity gene (cdi). From the nucleotide sequence it was deduced that colicin D had a molecular weight of 74683D and that the immunity protein had a molecular weight of 10057D. The amino-terminal portion of colicin D was found to be 96% homologous with the same region of colicin B. Both colicins share the same cell-surface receptor, FepA, and require the TonB protein for uptake. A putative TonB box pentapeptide sequence was identified in the amino terminus of the colicin D protein sequence. Since colicin D inhibits protein synthesis, it was unexpected that no homology was found between the carboxy-terminal part of this colicin and that of the protein synthesis inhibiting colicin E3 and cloacin DF13. This could indicate that colicin D does not function in the same manner as the latter two bacteriocins. The observed homology with colicin B supports the domain structure concept of colicin organization. The structural organization of the colicin operon is discussed. The extensive amino-terminal homology between colicins D and B, and the strong carboxy-terminal homology between colicins B, A, and N suggest an evolutionary assembly of colicin genes from a few DNA fragments which encode the functional domains responsible for colicin activity and uptake.