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1.
We have evaluated codon usage bias in Drosophila histone genes and have
obtained the nucleotide sequence of a 5,161-bp D. hydei histone gene repeat
unit. This repeat contains genes for all five histone proteins (H1, H2a,
H2b, H3, and H4) and differs from the previously reported one by a second
EcoRI site. These D. hydei repeats have been aligned to each other and to
the 5.0-kb (i.e., long) and 4.8-kb (i.e., short) histone repeat types from
D. melanogaster. In each species, base composition at synonymous sites is
similar to the average genomic composition and approaches that in the small
intergenic spacers of the histone gene repeats. Accumulation of synonymous
changes at synonymous sites after the species diverged is quite high. Both
of these features are consistent with the relatively low codon usage bias
observed in these genes when compared with other Drosophila genes. Thus,
the generalization that abundantly expressed genes in Drosophila have high
codon bias and low rates of silent substitution does not hold for the
histone genes.
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A chitinase-producing bacterium, designated WS7b, was isolated from a soil sample obtained from a black-pepper plantation
on Bangka Island, Indonesia. Fatty-acid methyl-ester analysis indicated that the isolate was Aeromonas caviae. A chitinase gene from WS7b was cloned in a pUC19-based plasmid vector, but without its natural promoter. The complete nucleotide
sequence of the gene was determined, and the structural gene consisted of a 2748-bp region encoding 864 amino acids. DNA sequence
analysis indicated that the gene had been cloned without its promoter, and this was confirmed by chitinase-plate assay of
the truncated version of the gene in Escherichia coli. The chitinase gene product showed amino-acid sequence similarity to chiA from A. caviae. Chitinase enzyme activity was determined spectrophotometrically, using colloidal chitin azure as substrate for extracellular
and intracellular fractions. The ability of the chitinase cloned in E. coli to hydrolyze chitin was less than that of the enzyme in its indigenous host. 相似文献
4.
Acceptor specificity of the human leukocyte alpha3 fucosyltransferase: role of FucT-VII in the generation of selectin ligands 总被引:2,自引:2,他引:0
Britten CJ; van den Eijnden DH; McDowell W; Kelly VA; Witham SJ; Edbrooke MR; Bird MI; de Vries T; Smithers N 《Glycobiology》1998,8(4):321-327
The alpha3 fucosyltransferase, FucT-VII, is one of the key
glycosyltransferases involved in the biosynthesis of the sialyl Lewis X
(sLex) antigen on human leukocytes. The sialyl Lewis X antigen
(NeuAcalpha(2-3)Galbeta(1-4)[Fucalpha(1-3)]GlcNAc-R) is an essential
component of the recruitment of leukocytes to sites of inflammation,
mediating the primary interaction between circulating leukocytes and
activated endothelium. In order to characterize the enzymatic properties of
the leukocyte alpha3 fucosyltransferase FucT-VII, the enzyme has been
expressed in Trichoplusia ni insect cells. The enzyme is capable of
synthesizing both sLexand sialyl-dimeric-Lexstructures in vitro , from
3'-sialyl-lacNAc and VIM-2 structures, respectively, with only low levels
of fucose transfer observed to neutral or 3'-sulfated acceptors. Studies
using fucosylated NeuAcalpha(2-3)-(Galbeta(1- 4)GlcNAc)3-Me acceptors
demonstrate that FucT-VII is able to synthesize both di-fucosylated and
tri-fucosylated structures from mono- fucosylated precursors, but
preferentially fucosylates the distal GlcNAc within a polylactosamine
chain. Furthermore, the rate of fucosylation of the internal GlcNAc
residues is reduced once fucose has been added to the distal GlcNAc. These
results indicate that FucT-VII is capable of generating complex selectin
ligands, in vitro , however the order of fucose addition to the lactosamine
chain affects the rate of selectin ligand synthesis.
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5.
Survival and Epiphytic Fitness of a Nonpathogenic Mutant of Xanthomonas campestris pv. Glycines 下载免费PDF全文
Xanthomonas campestris pv. glycines is the causal agent of bacterial pustule disease of soybeans. The objective of this work was to construct a nonpathogenic mutant derived from the pathogenic wild-type strain YR32 and to evaluate its effectiveness in preventing growth of its parent on the soybean phyllosphere. A mini-Tn5-derived transposon was used to generate nonpathogenic mutants. Southern hybridization and pulsed-field gel electrophoresis confirmed the presence of a single transposon in each of the nonpathogenic mutants. One of the nonpathogenic mutants, M715, failed to induce a hypersensitive response in tomato leaves. An ice nucleation gene (inaZ) carried in pJL1703 was introduced into strain YR32 as a reporter gene to demonstrate that the presence of M715 could reduce colonization of the soybean phyllosphere by YR32. de Wit serial replacement analysis showed that M715 competed equally with its wild-type parental strain, YR32. Epiphytic fitness analysis of YR32 in the greenhouse indicated that the population dynamics of strains YR32, YR32(pJL1703), and M715 were similar, although the density of the mutant was slightly less than that of its parent. The M715 mutant was able to survive for 16 days after inoculation on soybean leaves and maintained population densities of approximately 104 to 105 cells g (fresh weight) of leaf−1. Therefore, M715 shows promise as an effective biocontrol agent for bacterial pustule disease in soybeans. 相似文献
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We have identified a novel N -acetylgalactosaminyltransferase activity in
lactating bovine mammary gland membranes. Acceptor specificity studies and
analysis of products obtained in vitro by 400 MHz1H-NMR spectroscopy
revealed that the enzyme catalyses the transfer of N - acetylgalactosamine
(GalNAc) from UDP-GalNAc to acceptor substrates carrying a terminal,
beta-linked N -acetylglucosamine (GlcNAc) residue and establishes a
beta1-->4-linkage forming a GalNAcbeta1-->4GlcNAc ( N, N
'-diacetyllactosediamine, lacdiNAc) unit. Therefore, the enzyme can be
identified as a UDP-GalNAc:GlcNAcbeta-R beta1-->4-N-
acetylgalactosaminyltransferase (beta4-GalNAcT). This enzyme resembles
invertebrate beta4-GalNAcT as well as mammalian beta4-
galactosyltransferase (beta4-GalT) in acceptor specificity. It can,
however, be clearly distinguished from the pituitary hormone-specific
beta4-GalNAcT by its incapability of acting with an elevated activity on a
glycoprotein substrate carrying a hormone-specific peptide motif.
Furthermore, the GalNAcT activity appeared not to be due to a promiscuous
action of a beta4-GalT as could be demonstrated by comparing the
beta4-GalNAcT and beta4-GalT activities of the mammary gland, bovine
colostrum, and purified beta4-GalT, by competition studies with UDP-GalNAc
and UDP-Gal, and by use of an anti-beta4-GalT polyclonal inhibiting
antibody. Interestingly, under conditions where mammalian beta4-GalT forms
with alpha-lactalbumin (alpha-LA) the lactose synthase complex, the mammary
gland beta4-GalNAcT was similarly induced by alpha-LA to act on Glc with an
increased efficiency yielding the lactose analog GalNAcbeta1-->4Glc.
This enzyme thus forms the second example of a mammalian
glycosyltransferase the specificity of which can be modified by this milk
protein. It is proposed that the mammary gland beta4-GalNAcT functions in
the synthesis of lacdiNAc- based, complex-type glycans frequently occurring
on bovine milk glycoproteins. The action of this enzyme is to be considered
when aiming at the production of properly glycosylated protein
biopharmaceuticals in the milk of transgenic dairy animals.
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8.
Fucose is a major constituent of the protein- and lipid-linked glycans of
the various life-cycle stages of schistosomes. These fucosylated glycans
are highly antigenic and seem to play a role in the pathology of
schistosomiasis. In this article we describe the identification and
characterization of two fucosyltransferases (FucTs) in cercariae of the
avian schistosome Trichobilharzia ocellata, a GDP-Fuc:[Galbeta1--
>4]GlcNAcbeta-R alpha1-->3-FucT and a novel GDP-Fuc:Fucalpha-R
alpha1-- >2-FucT. Triton X-100 extracts of cercariae were assayed for
FucT activity using a variety of acceptor substrates. Type 1 chain
(Galbeta1- ->3GlcNAc) based compounds were poor acceptors, whereas those
based on a type 2 chain (Galbeta1-->4GlcNAc), whether
alpha2'-fucosylated, alpha3'-sialylated, or unsubstituted, and whether
present as oligosaccharide or contained in a glycopeptide or glycoprotein,
all served as acceptor substrates. In this respect the schistosomal alpha3-
FucT resembles human FucT V and VI rather than other known FucTs. N-
ethylmaleimide, an inhibitor of several human FucTs, had no effect on the
activity of the schistosomal alpha3-FucT, whereas GDP-beta-S was strongly
inhibitory. Large scale incubations were carried out with
Galbeta1-->4GlcNAc, GalNAcbeta1-->4GlcNAcbeta-O -(CH2)8COOCH3 and
Fucalpha1-->3GlcNAcbeta1-->2Man as acceptor substrates and the
products of the incubations were isolated using a sequence of
chromatographic techniques. By methylation analysis and 2D-TOCSY and
ROESY1H-NMR spectroscopy the products formed were shown to be Galbeta1--
>4[Fucalpha1-->2Fucalpha1-->3]GlcNAc,
GalNAcbeta1-->4[Fucalpha1-- >2Fucalpha1-->3]GlcNAcbe
ta-O-(CH2)8COOCH3, and Fucalpha1-->2Fucalpha1--
>3GlcNAcbeta1-->2Man, respectively. It is concluded that the alpha2-
FucT and alpha3-FucT are involved in the biosynthesis of the (oligomeric)
Lewisx sequences and the Fucalpha1-->2Fucalpha1-->3GlcNAc structural
element that have been described on schistosomal glycoconjugates.
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9.
A covariotide model explains apparent phylogenetic structure of oxygenic photosynthetic lineages 总被引:17,自引:13,他引:4
Lockhart PJ; Steel MA; Barbrook AC; Huson DH; Charleston MA; Howe CJ 《Molecular biology and evolution》1998,15(9):1183-1188
The aims of the work were (1) to develop statistical tests to identify
whether substitution takes place under a covariotide model in sequences
used for phylogenetic inference and (2) to determine the influence of
covariotide substitution on phylogenetic trees inferred for photosynthetic
and other organisms. (Covariotide and covarion models are ones in which
sites that are variable in some parts of the underlying tree are invariable
in others and vice versa.) Two tests were developed. The first was a
contingency test, and the second was an inequality test comparing the
expected number of variable sites in two groups with the observed number.
Application of these tests to 16S rDNA and tufA sequences from a range of
nonphotosynthetic prokaryotes and oxygenic photosynthetic prokaryotes and
eukaryotes suggests the occurrence of a covariotide mechanism. The degree
of support for partitioning of taxa in reconstructed trees involving these
organisms was determined in the presence or absence of sites showing
particular substitution patterns. This analysis showed that the support for
splits between (1) photosynthetic eukaryotes and prokaryotes and (2)
photosynthetic and nonphotosynthetic organisms could be accounted for by
patterns arising from covariotide substitution. We show that the additional
problem of compositional bias in sequence data needs to be considered in
the context of patterns of covariotide/covarion substitution. We argue that
while covariotide or covarion substitution may give rise to
phylogenetically informative patterns in sequence data, this may not always
be so.
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10.