Identification and characterization of the sodA genes encoding manganese superoxide dismutases in Vibrio parahaemolyticus, Vibrio mimicus, and Vibrio vulnificus

Sequencing of Fur titration assay-positive clones obtained from genomic DNA libraries of Vibrio parahaemolyticus, V. mimicus and V. vulnificus revealed open reading frames encoding proteins of 202, 205 and 202 amino acid residues, respectively. Each open reading frame was preceded by a predicted Fur box which overlaps a likely promoter with similarity to the -10 and -35 consensus sequence of Escherichia coli. The deduced amino acid sequences shared considerable homology with bacterial Mn-containing superoxide dismutases (MnSODs). Consistent with this, these Vibrio strains produced proteins with SOD activity resistant to inhibition by H2O2 and KCN only when grown under iron-limiting conditions. Primer extension analysis of the total RNA from these vibrios revealed iron-repressible expression of the genes. Furthermore, when grown under iron-limiting conditions, E. coli carrying a plasmid with each cloned gene overexpressed protein with the same electrophoretic mobility and insensitivity of SOD activity to H2O2 and KCN. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis followed by N-terminal amino acid sequencing revealed that proteins (MnSODs) having N-terminal amino acid sequences consistent with those deduced from the corresponding genes were present in cell lysates of the vibrios grown under these iron-limited conditions. These results demonstrate that the genes cloned in this study are sodA homologs encoding MnSODs, whose expression is regulated by the iron status of the growth medium. PCR using a primer set based on the V. parahaemolyticus sodA sequence revealed the presence of homologous genes in certain other Vibrio species.     

Genetic transformation of Populus genotypes with different chimaeric gene constructs: transformation efficiency and molecular analysis

Aspen (Populus tremula) and hybrid aspen (P. tremula × P. tremuloides) were transformed with different gene constructs using two types of promoter. The aim was to determine the influence of the reporter gene rolC, controlled by promoters of viral or plant origin, on genetic and morphologic expression of different transgenic aspen clones. An improved transformation method using leaf discs was developed, by which putative transgenic plantlets were regenerated at high efficiencies (up to 34%) on kanamycin-containing medium. Transgenic aspen carrying the rolC gene from Agrobacterium rhizogenes under control of the cauliflower-35S-promoter are reduced in size with smaller leaves, whereas aspen transgenic for the same rolC gene, but under control of the light inducible rbcS promoter from potato, are only slightly reduced in size compared to untransformed controls. However, all clones carrying 35S-rolC and rbcS-rolC genes revealed light-green colouration of leaves when compared to untransformed aspen. Owing to this special feature, constructs were used in which expression of the rolC gene was inhibited by insertion of a transposable element, Ac, from maize. Transgenic aspen transformed with the 35S-Ac-rolC and rbcS-Ac-rolC genes were morphologically similar to untransformed aspen, but out of 54 independently regenerated 35S-Ac-rolC transgenic aspen clones, 30 clones showed light-green/dark green variegated leaves. In contrast, out of 19 independently transformed rbcS-Ac-rolC aspen clones, only two clones revealed light-green/dark green variegated leaves. The role of bacterial strains in transformation, and molecular genetics of transgenic aspen plants (including the function of the transposable element, Ac, in the aspen genome) are discussed     

Exploration of the extracellular space by a large-scale secretion screen in the early Xenopus embryo

Secreted proteins play a crucial role in intercellular communication during embryogenesis and in the adult. We recently described a novel method, designated as secretion cloning, that allows identifying extracellular proteins exclusively based on their ability to be secreted by transfected cells. In this paper, we present the results of a large-scale screening of more than 90,000 clones from three cDNA expression libraries constructed from early Xenopus embryos. Of 170 sequenced clones, 65 appeared to encode secreted proteins; 26 clones (40%) were identical to previously known Xenopus genes, 25 clones (38%) were homologous to other genes identified in various organisms and 14 clones (22%) were novel. Apart from these bona fide secreted proteins, we also isolated lysosomal or other secretory pathway proteins and some cytoplasmic proteins commonly found in body fluids. Among the novel secreted proteins were two putative growth factors of the Granulin family, termed xGra1 and xGra2; they are structurally similar to EGF and TGFalpha and show a spotted expression pattern in the epidermis. Another secreted protein, designated xSOUL, belongs to the family of heme-binding proteins and exhibits distinct expression in the early brain. A third protein, termed Xystatin, is related to cysteine proteinase inhibitors. Our results indicate that secretion cloning is an effective and generally useful tool for the unbiased isolation of secreted proteins.     

Characterization of the mcrBC region of Escherichia coli K-12 wild-type and mutant strains.

We have carried out an analysis of the Escherichia coli K-12 mcrBC locus in order to (1) elucidate its genetic organization, (2) to identify the proteins encoded by this region, and (3) to characterize their involvement in the restriction of DNA containing methylated cytosine residues. In vitro expression of recombinant plasmids carrying all or portions of the mcrBC region revealed that the mcrB and mcrC genes are organized as an operon. The mcrBC operon specifies five proteins, as evident from parallel in vitro and in in vivo expression studies. Three proteins of 53, 35 and 34 kDa originate from mcrB expression, while two proteins of 37 and 16 kDa arise from mcrC expression. Products of both the mcrB and mcrC genes are required to restrict the methylated substrate DNA used in this study. We also determined the nature of mutant mcrBC loci in comparison to the E. coli K-12 wild-type mcrBC locus. A major goal of these studies was to clarify the nature of the mcrB-1 mutation, which is carried by some strains employed in previous analyses of the E. coli K-12 McrBC system. Based on our analyses the mutant strains investigated could be divided into different complementation groups. The mcrB-1 mutation is a nonsense or frameshift mutation located within mcrB. It causes premature termination of mcrB gene product synthesis and reduces the level of mcrC gene expression. This finding helps to understand an existing conflict in the literature. We also describe temperature-sensitive McrA activity in some of the strains analysed and its relationship to the previously defined differences in the tolerance levels of E. coli K-12 mcrBC mutants to cytosine methylation.     

Cloning of the fructan biosynthesis pathway of Jerusalem artichoke

To study the regulation of fructan synthesis in plants, we isolated two full-size cDNA clones encoding the two enzymes responsible for fructan biosynthesis in Jerusalem artichoke ( Helianthus tuberosus ): 1-sucrose:sucrose fructosyl transferase (1-SST) and 1-fructan:fructan fructosyl transferase (1-FFT). Both enzymes have recently been purified to homogeneity from Jerusalem artichoke tubers (Koops and Jonker (1994) J. Exp. Bot. 45, 1623–1631; Koops and Jonker (1996) Plant Physiol. 110, 1167–1175) and their amino acid sequences have been partially determined. Using RT–PCR and primers based on these sequences, specific fragments of the genes were amplified from tubers of Jerusalem artichoke. These fragments were used as probes to isolate the cDNAs encoding 1-SST and 1-FFT from a tuber-specific λZAP library. The deduced amino acid sequences of both cDNAs perfectly matched the sequences of the corresponding purified proteins. At the amino acid level, the cDNA sequences showed 61% homology to each other and 59% homology to tomato vacuolar invertase. Based on characteristics of the deduced amino acid sequence, the first 150 bp of both genes encode a putative vacuolar targeting signal. Southern blot hybridization revealed that both 1-SST and 1-FFT are likely to be encoded by single-copy genes. Expression studies based on RNA blot analysis showed organ-specific and developmental expression of both genes in growing tubers. Lower expression was detected in flowers and in stem. In other organs, including leaf, roots and dormant tubers, no expression could be detected. In tubers, the spatial and developmental expression correlates with the accumulation of fructans. Using the 1-sst and 1-fft cDNAs, chimeric genes were constructed driven by the CaMV 35S promoter. Analysis of transgenic petunia plants carrying these constructs showed that both cDNAs encode functional fructosyltransferase enzymes. Plants transformed with the 35S- 1-sst construct accumulated the oligofructans 1-kestose (GF₂), 1,1-nystose (GF₃) and 1,1,1-fructosylnystose (GF₄). Plants transformed with the 35S- 1-fft construct did not accumulate fructans, probably because of the absence of suitable substrates for 1-FFT, i.e. fructans with a degree of polymerization ≥ 3 (GF₂, GF₃, etc.). Nevertheless, protein extracts from these transgenic plants were able to convert GF₃, when added as a substrate, into fructans with a higher degree of polymerization. Progeny of crosses between a 35S- 1-sst -containing plant and a 35S- 1-fft- containing plant, showed accumulation of high-molecular-weight fructans in old, senescent leaves. Based on the comparison of the predicted amino acid sequences of 1-sst and 1-fft with those of other plant fructosyl transferase genes, we postulate that both plant fructan genes have evolved from plant invertase genes.     

Ly-49 multigene family. New members of a superfamily of type II membrane proteins with lectin-like domains

Ly-49 (YE1/48, A1) is a dimer protein expressed on subpopulations of murine NK cells. It is a member of a superfamily of type II transmembrane proteins containing carbohydrate recognition domains (CRD). In the mouse genome, the detection of multiple restriction fragments that cross-hybridize with Ly-49 cDNA probes suggests the presence of related genes. In this study, we have isolated several genomic clones encoding portions of CRD sequences highly homologous to the CRD of Ly-49. By using primers based on the consensus sequences of the genomic clones, expression of Ly-49-related genes was detected by the polymerase chain reaction in various organs, including lung, kidney, liver, spleen, and thymus. Two full-length cDNA clones that are highly homologous to the Ly-49 gene were subsequently isolated from a lung cDNA library. At the nucleotide level, the two clones are 72% and 80% identical to Ly-49 in their translated regions, but their sequences are different from those of the genomic clones characterized to date. The two cDNA clones potentially encode type II transmembrane proteins containing CRD that are very similar to Ly-49. These amino acid sequences are also homologous to other members of the superfamily of CRD-containing type II transmembrane proteins, including hepatic lectins and the low affinity IgER (CD23). The homology is most evident in the CRD but is also significant in other domains. These results demonstrate the existence of several functional genes that are highly related to Ly-49. These genes comprise a subfamily within the superfamily of type II transmembrane proteins containing CRD.     

Map-based cloning of a fertility restorer gene, Rf-1, in rice (Oryza sativa L.)

A rice nuclear gene, Rf-1, restores the pollen fertility disturbed by the BT-type male sterile cytoplasm, and is widely used for commercial seed production of japonica hybrid varieties. Genomic fragments carrying Rf-1 were identified by conducting chromosome walking and a series of complementation tests. Isolation and analysis of cDNA clones corresponding to the fragments demonstrated that Rf-1 encodes a mitochondrially targeted protein containing 16 repeats of the 35-aa pentatricopeptide repeat (PPR) motif. Sequence analysis revealed that the recessive allele, rf-1, lacks one nucleotide in the putative coding region, presumably resulting in encoding a truncated protein because of a frame shift. Rice Rf-1 is the first restorer gene isolated from cereal crops that has the property of reducing the expression of the cytoplasmic male sterility (CMS)-associated mitochondrial gene like many other restorer genes. The present findings may facilitate not only elucidating the mechanisms of male sterility by the BT cytoplasm and its restoration by Rf-1 but also isolating other restorer genes from cereal crops, especially rice.     

Proline dehydrogenase from Escherichia coli K12. Properties of the membrane-associated enzyme

The pattern of protein synthesis in hepatoma cell clones was analysed by two-dimensional separation of [35S]methionine-labelled proteins. The clones were derived from the differentiated Reuber H 35 hepatoma and showed differences in the expression of a number of liver-specific functions and the resistance to the growth-inhibitory effect of glucocorticoids. Five protein spots were observed in the extracts of the differentiated Faza 967 cells that were absent from the electrophoretogram of the dedifferentiated H 56 cells. This clone, on the other hand, displayed six spots absent from Faza 967 cells. The growth of both Faza 967 and H 56 cells was strongly inhibited by 1 microM dexamethasone. The dexamethasone-resistant clone 2, a dedifferentiated derivative of Faza 967 cells, synthesized two polypeptides that were not present in Faza 967 or H 56 cells and produced four polypeptides at a lower level than Faza 967 cells. The examination of the short-term effect of dexamethasone on protein synthesis in Faza 967 cells revealed nine induced and one repressed protein spots, which appeared to be in good agreement with earlier published data. It is concluded that dedifferentiation, although bringing about marked changes in certain liver-specific functions, such as enzyme activities or protein secretion, affects only a relatively small fraction of the genes expressed.     

Cloning, nucleotide sequence, and expression of the Pasteurella haemolytica A1 glycoprotease gene.

Pasteurella haemolytica serotype A1 secretes a glycoprotease which is specific for O-sialoglycoproteins such as glycophorin A. The gene encoding the glycoprotease enzyme has been cloned in the recombinant plasmid pH1, and its nucleotide sequence has been determined. The gene (designated gcp) codes for a protein of 35.2 kDa, and an active enzyme protein of this molecular mass can be observed in Escherichia coli clones carrying pPH1. In vivo labeling of plasmid-encoded proteins in E. coli maxicells demonstrated the expression of a 35-kDa protein from pPH1. The amino-terminal sequence of the heterologously expressed protein corresponds to that predicted from the nucleotide sequence. The glycoprotease is a neutral metalloprotease, and the predicted amino acid sequence of the glycoprotease contains a putative zinc-binding site. The gene shows no significant homology with the genes for other proteases of procaryotic or eucaryotic origin. However, there is substantial homology between gcp and an E. coli gene, orfX, whose product is believed to function in the regulation of macromolecule biosynthesis.     

Novel molecular features of the fibrolytic intestinal bacterium Fibrobacter intestinalis not shared with Fibrobacter succinogenes as determined by suppressive subtractive hybridization

Suppressive subtractive hybridization was conducted to identify unique genes coding for plant cell wall hydrolytic enzymes and other properties of the gastrointestinal bacterium Fibrobacter intestinalis DR7 not shared by Fibrobacter succinogenes S85. Subtractive clones from F. intestinalis were sequenced and assembled to form 712 nonredundant contigs with an average length of 525 bp. Of these, 55 sequences were unique to F. intestinalis. The remaining contigs contained 764 genes with BLASTX similarities to other proteins; of these, 80% had the highest similarities to proteins in F. succinogenes, including 30 that coded for carbohydrate active enzymes. The expression of 17 of these genes was verified by Northern dot blot analysis. Of genes not exhibiting BLASTX similarity to F. succinogenes, 30 encoded putative transposases, 6 encoded restriction modification genes, and 45% had highest similarities to proteins in other species of gastrointestinal bacteria, a finding suggestive of either horizontal gene transfer to F. intestinalis or gene loss from F. succinogenes. Analysis of contigs containing segments of two or more adjacent genes revealed that only 35% exhibited BLASTX similarity and were in the same orientation as those of F. succinogenes, indicating extensive chromosomal rearrangement. The expression of eight transposases, and three restriction-modification genes was confirmed by Northern dot blot analysis. These data clearly document the maintenance of carbohydrate active enzymes in F. intestinalis necessitated by the preponderance of polysaccharide substrates available in the ruminal environment. It also documents substantive changes in the genome from that of F. succinogenes, which may be related to the introduction of the array of transposase and restriction-modification genes.     

Screening of environmental DNA libraries for the presence of genes conferring lipolytic activity on Escherichia coli

Environmental DNA libraries prepared from three different soil samples were screened for genes conferring lipolytic activity on Escherichia coli clones. Screening on triolein agar revealed 1 positive clone out of 730,000 clones, and screening on tributyrin agar revealed 3 positive clones out of 286,000 E. coli clones. Substrate specificity analysis revealed that one recombinant strain harbored a lipase and the other three contained esterases. The genes responsible for the lipolytic activity were identified and characterized.