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J L Slightom

Publications and source records attributed to J L Slightom.

At least 91 records · Page 5Linked to original sources
PubMed1989

Molecular phylogeny of the family of apes and humans.

The morphological picture of primate phylogeny has not unambiguously identified the nearest outgroup of Anthropoidea and has not resolved the branching pattern within Hominoidea. The molecular picture provides more resolution and clarifies the systematics of Hominoidea. Protein and DNA evidence divides Hominoidea into Hylobatidae (gibbons) and Hominidae, family Hominidae into Ponginae (orangutan) and Homininae, and subfamily Homininae into two tribes, one for Gorilla, and the other for Pan (chimpanzee) and Homo. Parsimony and maximum likelihood analyses, carried out on orthologous noncoding nucleotide sequences from primate beta-globin gene clusters, provide significant evidence for the human-chimpanzee tribe and overwhelming evidence for the human-chimpanzee-gorilla clade. These analyses also indicate that the rate of molecular evolution became slower in hominoids than in other primates and mammals.

Animals↗
PubMed1988

Embryonic epsilon and gamma globin genes of a prosimian primate (Galago crassicaudatus). Nucleotide and amino acid sequences, developmental regulation and phylogenetic footprints.

Sequence analysis of epsilon and gamma genes and encoded globins and high-pressure liquid chromatography analysis of globin compositions in blood hemolysates obtained from embryos, fetuses and adults show that the prosimian primate Galago crassicaudatus expresses its epsilon and gamma genes only embryonically. Since rabbit, mouse and galago all have embryonic gamma genes but simian primates have fetal gamma genes, we conclude that gamma E evolved into gamma F in stem-simians. An elevated non-synonymous substitution rate characterizes this transition. The alignment of epsilon and gamma nucleotide sequences and the parsimoniously reconstructed evolutionary history of these sequences identify several anciently conserved cis-regulatory elements (phylogenetic footprints) important for gamma expression in primates and also cis-mutations which may have been involved in the recruitment of the gamma gene to a fetal program in simian primates.

Amino Acid Sequence↗
PubMed1988

Rhesus fetal globin genes. Concerted gene evolution in the descent of higher primates.

The comparison of the nucleotide sequences of closely linked duplicated genes of higher eukaryotes has been important in the identification of molecular events that shape the evolution of mammalian genes, most notably recombinational events such as unequal crossovers and gene conversions. Toward this goal we have been comparing the nucleotide sequences of the paired gamma 1- and gamma 2-fetal globin genes from species of catarrhine primates. Previous comparisons document that, within each great ape species as in humans, the paired gamma-genes have been involved in gene conversion events. We now extend our analysis to the catarrhine superfamily Cercopithecoidea by obtaining the nucleotide sequence of the paired gamma 1- and gamma 2-genes of rhesus monkey (Macaca mulatta). The rhesus gamma 1- and gamma 2-genes diverge less from each other than from human, chimpanzee, gorilla, and orangutan gamma 1- or gamma 2-genes. This finding indicates that a species-specific gene conversion occurred between rhesus gamma 1- and gamma 2-genes. This gamma-gene conversion (labeled C14 in our series) involved at least 1898 base pairs, extending across the complete transcriptional region of the rhesus gamma-genes. C14 could have resulted from a single large conversion or several short conversion events which may have involved the (TG)n repetitive sequence element. Parsimony analysis of the enlarged body of gamma-gene sequence data also strengthens the evidence for the 14 previously suggested gamma-gene conversion events: labeled C2, C3, and C4 in Homo; C5, C6, and C7 in Pan; C8, C9, and C10 in Gorilla; C11, C12, C13 in Pongo; C1 in the stem to Homininae (the subfamily of Homo, Pan, and Gorilla) and CO in the stem of Hominidae (the family of Pongo and Homininae).

Amino Acid Sequence↗
PubMed1988

Human plasminogen activator inhibitor-1 gene. Promoter and structural gene nucleotide sequences.

We have determined the nucleotide sequence of the human plasminogen activator inhibitor-1 (PAI-1) gene and significant stretches of DNA which extend into its 5'-and 3'-flanking DNA regions; a total sequence of 15,867 base pairs (bp) is presented. The sequenced 5'-flanking DNA (1,520 bp) contains the essential eukaryotic cis-type proximal regulatory elements CCAAT and TATAA; the more distal 5'-flanking DNA region, as well as some introns, contain sequence elements which share identities with known eukaryotic enhancer elements. A major finding is the identification of a large region of shared nucleotides (comprising of about 520 bp) between the 5'-flanking DNAs of PAI-1 and tissue-type plasminogen activator genes. The length of the PAI-1 5'-untranslated region was found to be 145 bp as determined by nuclease analysis. The remaining PAI-1 structural gene consists of amino acid coding regions (containing a total of 1,206 bp, coding for the 23 amino acids of the signal peptide and 379 amino acids of the mature PAI-1 protein), 8 intron regions (a total of 8,978 bp), and a long 3'-untranslated region of about 1,800 bp which contains several polyadenylation sites. Two types of repetitive DNA elements are located within the PAI-1 structural gene and flanking DNAs: we have found 12 Alu elements and 5 repeats of a long poly (Pur) element. These Alu-Pur elements may represent a subset of the more abundant Alu family of repetitive sequence elements.

Amino Acid Sequence↗
PubMed1988

Nucleotide sequence of a mutation in the proB gene of Escherichia coli that confers proline overproduction and enhanced tolerance to osmotic stress.

We determined the nucleotide (nt) sequence of a mutation that confers proline overproduction and enhanced tolerance of osmotic stress on bacteria. The mutation, designated as proB74, is an allele of the Escherichia coli proB gene which results in a loss of allosteric regulation of the protein product, gamma-glutamyl kinase. Our sequencing indicated that the proB74 mutation is a substitution of an A for a G at nt position 319 of the coding strand of the gene, resulting in a change of an aspartate to an asparagine at amino acid (aa) residue 107 of the predicted protein product. Rushlow et al. [Gene 39 (1984) 109-112] determined that another proB mutation (designated as DHPR), that resulted in a loss of allosteric inhibition by proline of the E. coli gamma-glutamyl kinase, was due to a substitution of an alanine for a glutamate at aa residue 143. Therefore, even though both the DHPR and the proB74 mutations caused a loss of allosteric inhibition of gamma-glutamyl kinase, they are due to different amino acid substitutions.

Alleles↗
PubMed1988

The spider monkey psi eta-globin gene and surrounding sequences: recent or ancient insertions of LINEs and SINEs?

A phylogenetic comparison of the psi eta-globin DNA sequence of the spider monkey (Ateles geoffroyi) to orthologous sequences from other primates provides evidence for an evolutionarily recent (less than 17 million years ago (MYA] insertion of a truncated L1 LINE (long interspersed repetitive element). An Alu SINE (short interspersed element), found 3 kb downstream of the poly(A) addition site, arose less than 40 MYA subsequent to the divergence of platyrrhinies (New World monkeys) from catarrhines (humans, apes, and Old World monkeys). Another Alu element, which appears in the catarrhines 588 bp upstream from the psi eta gene, is absent in Ateles, thus placing its possible time of insertion between 20 and 40 MYA. Alignment of the Ateles psi eta sequence with orthologous hominoid sequences (M. M. Miyamoto, J. L. Slightom, and M. Goodman, 1987, Science 238: 369-373) provides unequivocal evidence against the view (J. H. Schwartz, 1987, "The Red Ape: Orang-utans and Human Origins," Houghton Mifflin, Boston, MA) that the orangutan forms a monophyletic group with human. Furthermore, a critical analysis of potential sources of homoplasy (i.e., parallel evolution) reaffirms a Homo-Pan monophyletic clade (Miyamoto et al., 1987). Reconstruction of primate psi eta sequence phylogeny suggests Ateles and Aotus shared a common ancestor only 16 +/- 1.5 MYA. Finally, the results show a mutation rate of 1.7 +/- 0.2 x 10(-9) mutations site-1 year-1 during the evolution of the Ateles psi eta-globin region since the divergence of catarrhines from platyrrhinies.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1988

Molecular systematics of higher primates: genealogical relations and classification.

We obtained 5' and 3' flanking sequences (5.4 kilobase pairs) from the psi eta-globin gene region of the rhesus macaque (Macaca mulatta) and combined them with available nucleotide data. The completed sequence, representing 10.8 kilobase pairs of contiguous noncoding DNA, was compared to the same orthologous regions available for human (Homo sapiens, as represented by five different alleles), common chimpanzee (Pan troglodytes), gorilla (Gorilla gorilla), and orangutan (Pongo pygmaeus). The nucleotide sequence for Macaca mulatta provided the outgroup perspective needed to evaluate better the relationships of humans and great apes. Pairwise comparisons and parsimony analysis of these orthologues clearly demonstrated (i) that humans and great apes share a high degree of genetic similarity and (ii) that humans, chimpanzees, and gorillas form a natural monophyletic group. These conclusions strongly favor a genealogical classification for higher primates consisting of a single family (Hominidae) with two subfamilies (Homininae for Homo, Pan, and Gorilla and Ponginae for Pongo).

Animals↗
PubMed1987

Phylogenetic relations of humans and African apes from DNA sequences in the psi eta-globin region.

Sequences from the upstream and downstream flanking DNA regions of the psi eta-globin locus in Pan troglodytes (common chimpanzee), Gorilla gorilla (gorilla), and Pongo pygmaeus (orangutan, the closest living relative to Homo, Pan, and Gorilla) provided further data for evaluating the phylogenetic relations of humans and African apes. These newly sequenced orthologs [an additional 4.9 kilobase pairs (kbp) for each species] were combined with published psi eta-gene sequences and then compared to the same orthologous stretch (a continuous 7.1-kbp region) available for humans. Phylogenetic analysis of these nucleotide sequences by the parsimony method indicated (i) that human and chimpanzee are more closely related to each other than either is to gorilla and (ii) that the slowdown in the rate of sequence evolution evident in higher primates is especially pronounced in humans. These results indicate that features (for example, knuckle-walking) unique to African apes (but not to humans) are primitive and that even local molecular clocks should be applied with caution.

Animals↗
PubMed1987

Orangutan fetal globin genes. Nucleotide sequence reveal multiple gene conversions during hominid phylogeny.

We have determined the nucleotide sequences of the linked gamma 1- and gamma 2- fetal globin genes from a single orangutan (Pongo pygmaeus) chromosome and compared them with the corresponding genes of other simian primates (gamma 1- and gamma 2-genes of human, chimpanzee, gorilla, and the single gamma-gene of the spider monkey). Previous studies have indicated that the two gamma-gene loci in catarrhine primates resulted from a duplication about 25-35 million years ago. However, comparisons of aligned gamma-gene sequences show that these genes contain three regions with distinct histories of which only the 3' third clearly reflects the ancestral nature expected of the gamma-gene duplication. To explain these different evolutionary histories and also hominid relationships we provide evidence for the occurrence of sequence conversions which affect region 1 (120 base pairs 5'-flanking through exon 2) in all hominid species and extend to varying degrees into region 2 (intron 2 through exon 3). Close examinations of the proposed conversions further suggest that 12 of the 13 conversions identified involved gamma 1 converting gamma 2. Polarity of these conversions may be a result of differential survival between these genes because during human fetal development the gamma 1-gene is preferentially expressed over the gamma 2-gene and it may be subjected to greater selection pressure to remain unaltered.

Animals↗
PubMed1987

Advances in the molecular biology of plant seed storage proteins.

Plant seed storage proteins were among the first proteins to be isolated (20); however, only recently, as a result of using molecular biology techniques, have the amino acid sequences of many of these proteins been determined. With the accumulation of amino acid sequence data for many vicilin-type storage proteins much has been learned concerning the location of conserved amino acid regions and other regions which can tolerate amino acid sequence variation. Combining this knowledge with recent advances in plant gene transfer technologies will allow molecular biologists to correct (by using amino acid replacement mutations) the sulfur amino acid deficiency inherent to bean seed storage proteins. The development of more nutritious soybean and common bean seeds will be of benefit to programs involving human and animal nutrition.

Journal Article↗
PubMed1987

Double-stranded cleavage of T-DNA and generation of single-stranded T-DNA molecules in Escherichia coli by a virD-encoded border-specific endonuclease from Agrobacterium tumefaciens.

The virD locus of Agrobacterium tumefaciens Ti plasmid pTiA6 was sequenced. Computer analysis of the sequence indicated five possible open reading frames (ORFs) within this locus. Two additional ORFs were identified distal to this locus. However, only two polypeptides of apparent molecular masses 16 and 56 kilodaltons, the products of ORFs 1 and 2, were detected in Escherichia coli, both in vivo and in an in vitro coupled transcription-translation system. The virD locus was cloned in expression vector pKK223.3 under control of a tac promoter and introduced into an E. coli strain harboring mini-Ti plasmid pAL1050. When induced with isopropyl-beta-D-thiogalactopyranoside, the virD gene products exhibited double-stranded T-DNA border-specific endonuclease activity. Deletion analysis demonstrated that this activity is encoded within the 5'-proximal 1.7-kilobase-pair portion of the virD locus that carries ORF 1 and most of ORF 2. Neither ORF 1 nor ORF 2 independently showed endonuclease activity; complementation studies indicated that the products of ORFs 1 and 2 together have this activity. The expression of this 1.7-kilobase-pair region of the virD locus caused double-stranded cleavage of the T-DNA at or near the borders and generated single-stranded T-DNA molecules with approximately equal frequencies in E. coli.

Amino Acid Sequence↗
PubMed1986

The glycosylated seed storage proteins of Glycine max and Phaseolus vulgaris. Structural homologies of genes and proteins.

Considerable information is now available concerning the 7 S seed storage proteins of legumes and the genes that encode them. Our study compares the gene encoding a beta-type subunit of phaseolin (Pvu beta), the 7 S protein of common bean (Phaseolus vulgaris), with the gene encoding an alpha'-subunit of beta-conglycinin (Gma alpha'), the 7 S protein of soybean (Glycine max). The comparison involves 2880 base pairs of Pvu beta and 3636 base pairs of Gma alpha' and includes approximately 1 kilobase pair of 5'-flanking sequences, and 5' and 3' untranslated sequences, as well as the six exons and five introns that are found to occur in similar positions in both genes. Conserved sequences in the 5'-flanking regions of these genes are discussed in light of their potential regulatory role. Published sequences for 7 S genes of pea (Pisum sativum) permit the inference of the nature and direction of evolutionary change and, in particular, show that the major size difference between the large Gma alpha' polypeptide and the smaller polypeptides of pea and common bean is due to a large insertion in the first exon of Gma alpha'. Comparisons of protein primary structure, potential glycosylation sites, and predicted protein hydropathy show that strongly conserved features of 7 S proteins cut across exon boundaries and that nonconserved regions exist that may have potential for protein modification.

Amino Acid Sequence↗
PubMed1986

Nucleotide sequence analysis of TL-DNA of Agrobacterium rhizogenes agropine type plasmid. Identification of open reading frames.

We have determined the nucleotide sequence of the Ri TL-DNA region from an Agrobacterium rhizogenes agropine-type plasmid using subcloned regions from the essentially identical Ri TL-DNAs from strains A4 and HRI. This sequenced region of 21,126 base pairs (bp) contains the complete TL-DNA region of the Ri plasmid as determined by analysis of TL-DNA borders in the genome of infected, clonal, Convolvulus arvensis plants. The left and right borders of the TL-DNA are flanked by 25-bp sequences which match the 25-bp terminal sequences found near the borders of T-DNA regions of Agrobacterium tumefaciens Ti plasmids. Other DNA sequences similar to these 25-bp terminal sequences are found within the TL region, and some of these sequences appear to be associated with Ri TL-DNA structures found in transformed tobacco plants. The TL-DNA region contains 18 open reading frames, many of which have 5' and 3' regulatory elements similar to those found in eukaryotic genes. In many cases, CCAAT and TATA elements were found upstream from putative transcriptional initiation codons, and poly(A) addition (AATAAA) elements were observed in presumed 3'-noncoding regions. Comparison of Ri TL-DNA coding and noncoding sequence regions with T-DNA sequence regions from octopine type Ti plasmid pTi15955 reveals no extensive sequence homologies.

Base Sequence↗
PubMed1986

Nucleotide sequence and evolution of the orangutan epsilon globin gene region and surrounding Alu repeats.

We have mapped and sequenced the epsilon globin gene and seven surrounding Alu repeat sequences in the orangutan beta globin gene cluster and have compared these and other orangutan sequences to orthologously related human sequences. Noncoding flanking and intron sequences, synonymous sites of alpha, gamma, and epsilon globin coding regions, and Alu sequences in human and orangutan diverge by 3.2%, 2.7%, and 3.7%, respectively. These values compare to 3.6% from DNA hybridizations and 3.4% from the psi eta globin gene region. If as suggested by fossil evidence and "molecular clock" calculations, human and orangutan lineages diverged about 10-15 MYA, the rate of noncoding DNA evolution in the two species is 1.0-1.5 X 10(-9) substitutions per site per year. We found no evidence for either the addition or deletion of Alu sequences from the beta globin gene cluster nor is there any evidence for recent concerted evolution among the Alu sequences examined. Both phylogenetic and phenetic distance analyses suggest that Alu sequences within the alpha and beta globin gene clusters arose close to the time of simian and prosimian primate divergence (about 50-60 MYA). We conclude that Alu sequences have been evolving at the rate typical of noncoding DNA for the majority of primate history.

Amino Acid Sequence↗
PubMed1986

Expression of a bean storage protein 'phaseolin minigene' in foreign plant tissues.

Using the phaseolin gene and its cDNA counterpart we constructed a mutant phaseolin gene lacking the five introns but retaining its natural 5' and 3' plant-regulatory sequences. This mutant phaseolin gene (minigene) was inserted into the Ti-plasmid of Agrobacterium tumefaciens strain 15955 which allowed its transfer and integration into the tobacco genome. Full-length and correctly initiated phaseolin mRNA was found among the poly(A)+RNA isolated from plant callus transformed with the minigene construction by using RNA-DNA hybridization and S1 nuclease mapping techniques. The presence of phaseolin polypeptides in soluble protein extracts from transformed tobacco tissues was confirmed by immunological methods. These results demonstrate that phaseolin gene introns and intron splicing are not a necessary requirement for biogenesis of stable phaseolin mRNA and that no alternative splice site was introduced by the removal of five introns.

Cloning, Molecular↗
PubMed1985

Isolation and identification of TL-DNA/plant junctions in Convolvulus arvensis transformed by Agrobacterium rhizogenes strain A4.

We have constructed a Charon 4A phage library containing insert DNA isolated from a morning glory (Convolvulus arvensis) plant (clone 7) regenerated from a root organ culture incited by Agrobacterium rhizogenes, strain A4. Using a subcloned region of the Ri plasmid as P-labeled probe, two lambda clones containing most of the 'left' T-DNA (TL) region were isolated. One of these lambda clones contains the left TL-DNA/plant junction, which was located by comparing nucleotide sequences from the appropriate regions of the Ri plasmid and this lambda clone. A 25-bp sequence found near this left TL-DNA/plant junction matches the 25-bp terminal sequence found at or near T-DNA/plant junctions of both nopaline- and octopine-type A. tumefaciens Ti plasmids. A possible location for the right Ri TL-DNA/plant junction in C. arvensis clone 7 was found by obtaining the nucleotide sequence surrounding its mapped location. Hybridization of plant DNA found adjacent to the left TL-DNA/plant junction against total C. arvensis DNA shows that this T-DNA integration occurred in a plant DNA region that does not contain highly repetitive DNA sequences. Nucleotide sequence analysis of 1004 bp of this plant DNA revealed no complete or partial open reading frames, but this plant DNA does have the potential to form various secondary structures which might play a role in the T-DNA integration event.

Journal Article↗
PubMed1985

Nucleotide sequences from phaseolin cDNA clones: the major storage proteins from Phaseolus vulgaris are encoded by two unique gene families.

The nucleotide sequences of eight partial and five full-length phaseolin cDNA clones show that phaseolin polypeptides are encoded by two distinct gene families which differ in their coding regions by the presence or absence of two different size direct repeats. The alpha-type phaseolin polypeptides are encoded by genes containing direct repeats which encode 14 additional amino acids. Aside from these differences, the alpha-and beta-type phaseolin genes show a high degree of homology (98%) which is consistent with these genes being derived from a common ancestral gene. Much of the heterogeneity found in the phaseolin polypeptides appears to be due to post-translational processing. Nucleotide sequence analysis demonstrates that the alpha-type genes contain only a few amino acid replacement substitutions and that the beta-type genes appear to contain no amino acid replacement substitutions. S1 nuclease mapping shows a complex pattern for transcriptional initiation of phaseolin mRNA. Hydropathy analysis shows that phaseolin polypeptides are predominately hydrophilic, and that the two N-glycosyl recognition sites are located in different hydropathic environments.

Amino Acid Sequence↗