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PubMed2004

Modulation of floral development by a gibberellin-regulated microRNA.

Floral initiation and floral organ development are both regulated by the phytohormone gibberellin (GA). For example, in short-day photoperiods, the Arabidopsis floral transition is strongly promoted by GA-mediated activation of the floral meristem-identity gene LEAFY. In addition, anther development and pollen microsporogenesis depend on GA-mediated opposition of the function of specific members of the DELLA family of GA-response repressors. We describe the role of a microRNA (miR159) in the regulation of short-day photoperiod flowering time and of anther development. MiR159 directs the cleavage of mRNA encoding GAMYB-related proteins. These proteins are transcription factors that are thought to be involved in the GA-promoted activation of LEAFY, and in the regulation of anther development. We show that miR159 levels are regulated by GA via opposition of DELLA function, and that both the sequence of miR159 and the regulation of miR159 levels by DELLA are evolutionarily conserved. Finally, we describe the phenotypic consequences of transgenic over-expression of miR159. Increased levels of miR159 cause a reduction in LEAFY transcript levels, delay flowering in short-day photoperiods, and perturb anther development. We propose that miR159 is a phytohormonally regulated homeostatic modulator of GAMYB activity, and hence of GAMYB-dependent developmental processes.

Agrobacterium tumefaciens↗

PubMed1987

The requirements for a high level of transposition of bacteriophage Mu.

To analyse the functional and structural requirements of Mu transposition a special mini-Mu transposon was constructed. This mini-Mu, situated on a derivative of pBR322, has an easily selectable marker gene conferring chloramphenicol resistance (Cam) cloned between the ends of the mini-Mu. The genes required for transposition are cloned outside the ends and are under control of the PL promoter of bacteriophage lambda. To obtain a high frequency of transposition the A and B products are required. Under B- conditions both cointegrate formation and simple insertions are strongly reduced. The role of B in the transposition process is unknown and is discussed. Deletion analysis of the ends of the mini-Mu has revealed the existence of multiple sites required for transposition. The same sites were found to be strong A-binding sites. In addition two weak A-binding sites were found. Point mutations introduced into these last sites show that they are at least as important for transposition as the strong binding sites. The organization of the binding sites is asymmetric in Mu. At the left end two binding sites are situated more than 100 bp away from the end. These affect specifically the frequency of transposition. The distance between these two sites and the site close to the left end is extremely critical. At the right end also three A-binding sites are found, but only two seem to be important for transposition. Transposition with low frequency can be obtained with a mini-Mu with only one end. Secondary att sites are selected which all show some homology with an A-binding site. An absolute requirement for a 5'T at the artificial end is observed. Based on these results a simple scheme for the evolution of a transposon is discussed.

Bacteriophages↗

PubMed1992

Two novel human pancreatic lipase related proteins, hPLRP1 and hPLRP2. Differences in colipase dependence and in lipase activity.

We have isolated cDNAs coding for two novel human pancreatic lipase (hPL)-related human proteins, referred to as hPL-related proteins 1 and 2 (hPLRP1 and hPLRP2) and for hPL. The two novel proteins show an amino acid sequence identity to hPL of 68 and 65% for hPLRP1 and 2, respectively. All three proteins are secreted into the medium after transfection of COS cells with the corresponding cDNAs. The size of the three expressed proteins is similar and ranges between 45 and 50 kDa. The expressed hPLRP2 shows a lipolytic activity that is, however, in contrast to that of hPL only marginally dependent on the presence of colipase, whereas hPLRP1 shows no activity in this assay. A Northern analysis of normal human pancreas mRNA shows that the expression levels of hPLRP1 and hPLRP2 are about 4-fold and 24-fold lower, respectively, than that of hPL. hPLRP2 is, additionally, most closely related to a lipase reported to be expressed in mouse T-cells. A comparison of the sequences of the three proteins with sequences described as pancreatic lipases of other animal species shows three subfamilies of closer kinship. This suggests that the two novel proteins also exist in other species and that some of the sequences reported to be pancreatic lipase might more likely be the orthologues of hPLRP1 or hPLRP2 in those species.

Amino Acid Sequence↗

PubMed1990

Evolution of the tryptophan synthetase of fungi. Analysis of experimentally fused Escherichia coli tryptophan synthetase alpha and beta chains.

During evolution of fungi, the separate tryptophan synthetase alpha and beta polypeptides of bacteria appear to have been fused in the order alpha-beta rather than the beta-alpha order that would be predicted from the order of the corresponding structural genes in all bacteria. We have fused the tryptophan synthetase polypeptides of Escherichia coli in both orders, alpha-beta and beta-alpha, with and without a short connecting (con) sequence, to explore possible explanations for the domain arrangement in fungi. We find that proteins composed of any of the four fused polypeptides, beta-alpha, beta-con-alpha, alpha-beta, and alpha-con-beta, are highly active enzymatically. However, only the alpha-beta and alpha-con-beta proteins are as active as the wild type enzyme. All four fusion proteins appear to be less soluble in vivo than the wild type enzyme; this abnormal characteristic is minimal for the alpha-con-beta enzyme. The alpha and beta domains of the four fusion polypeptides were not appreciably more heat labile than the wild type polypeptides. Competition experiments with mutant tryptophan synthetase alpha protein, and the fusion proteins suggest that in each fusion protein the joined alpha and beta domains have a functional tunnel connecting their alpha and beta active sites. Three tryptophan synthetase beta'-alpha fusion proteins were examined in which the carboxyl-terminal segment of the wild type beta polypeptide was deleted and replaced by a shorter, unnatural sequence. The resulting deletion fusion proteins were enzymatically inactive and were found predominantly in the cell debris. Evaluation of our findings in relation to the three-dimensional structure of the tryptophan synthetase enzyme complex of Salmonella typhimurium (5) and the results of mutational analyses with E. coli suggest that tryptophan synthetase may have evolved via an alpha-beta rather than a beta-alpha fusion because in beta-alpha fusions the amino-terminal helix of the alpha chain cannot assume the conformation required for optimal enzymatic activity.

Amino Acid Sequence↗

PubMed1981

The evolution of alpha-fetoprotein and albumin. II. The structures of the alpha-fetoprotein and albumin genes in the mouse.

The murine alpha-fetoprotein (AFP) and albumin genes have been cloned from genomic libraries derived from Balb/c DNA. By restriction endonuclease mapping and electron microscopy, we have shown that both genes are organized similarly into 15 coding segments interrupted by 14 intervening sequences. The sizes of the corresponding coding segments in each gene are identical, lending support to the hypothesis that the two genes, were derived from a common ancestral gene. However, no nucleotide homology between coding segments was observed. Both the sizes and the nucleotide sequence of flanking and intervening sequences have diverged significantly as well. Two regions of the AFP gene, 925 base pairs in the 5' flanking DNA and 180 base pairs in the third intervening sequence, hybridized to the same region of DNA in the third intervening sequence of albumin. The 180-base pair homologies within each gene are present in opposite orientation relative to the direction of transcription, and are associated with reiterated DNA. Thus, it is unlikely that they represent true sequence conservation. An examination of the sizes of the coding segments in each gene reveals a thrice repeated domain, consisting of 4 coding segments. We propose that these correspond to the three domains observed in several mammalian albumins, and in murine AFP.

Albumins↗

PubMed1990

The hok killer gene family in gram-negative bacteria.

The seven members of the hok killer gene family in Gram-negative bacteria are described here. The members of this gene family have been sequenced and include hok/sok from plasmid R1, flm and srnB from plasmid F, pnd from plasmids R483 and R16, and gef and relF, which are located on the Escherichia coli chromosome. The killer proteins encoded by these loci are highly toxic polypeptides of 50 to 52 amino acids. The proteins kill the cells from the inside by interfering with a vital function in the cell membrane. On the basis of their relatedness, the killer proteins and their corresponding loci are divided into four subfamilies. The members of one subfamily, hok/sok and flm, mediate plasmid maintenance by killing plasmid-free cells. The pnd and srnB subfamilies were discovered through their abilities to cause membrane damage and degradation of stable RNA. gef and relF, which constitute the chromosomal subfamily, were found because of their sequence similarity at the DNA and protein levels with other members of the hok gene family. However, no function has been described for the proteins belonging to this subfamily. Although the four subfamilies are distantly related in terms of DNA and protein sequence similarity, the overall genetic organization of the different loci has been well conserved during evolution. The expression of all of the members of the hok gene family is regulated post-transcriptionally. Thus, the expression of the hok and flm genes is regulated by small antisense RNAs that inhibit the translation of the stable hok and flm mRNAs. On the basis of structural and functional similarities, we suggest that each of the related plasmid-encoded killer genes is regulated by antisense RNAs. The conservation of this widespread gene family in Gram-negative bacteria suggests that the genes are important to the genomes that carry them.

Amino Acid Sequence↗

PubMedDate not supplied

[Beta-lactamases in laboratory and their role in resistance Part I.: Evolution of bacterial resistance mediated by beta-lactamases].

Beta-lactamases are the commonest cause of bacterial resistance to beta-lactam antibiotics. They have been classified phenotypically by their isoelectric point, substrate profile, susceptibility to inhibitors and genetic origin. Chromosomal beta-lactamases are typical for certain bacterial species and plasmid beta-lactamases are transferable between different species and genera. Sequencing of beta-lactamase genes enabled to divide them into four classes: A, B, C and D. The ability of a beta-lactamase to confer resistance depends on its location, kinetics, quantity and physicochemical conditions. First beta-lactamases were described soon after introduction of penicillin. Plasmid-mediated broad-spectrum beta-laktamases appeared in the middle 60-s of the XX century and confer resistance to penicillins and some first generation cephalosporins. They include TEM-1, TEM-2, SHV-1, ROB, BRO, OXA and PSE beta-lactamases and are transferred by conjugation between different species and strains of Gram-negative bacteria. The new beta-lactam agents nowadays are compromised mostly by extended-spectrum beta-lactamases, inhibitor-resistant beta-lactamases and carbapenemases. Extended-spectrum beta-lactamases (ESBLs) were described for the first time 20 years ago and are derived from the parental TEM and SHV-1 beta-lactamases by mutations that alter the configuration of the active site to expand their spectrum of activity. They hydrolyse oxymino-cephalosporins and aztreonam. The rapid and accurate laboratory detection of ESBLs is important for choosing appropriate antibiotic therapy. Infections caused by Enterobacteriaceae producing ESBLs pose a therapeutic problem due to multiple antibiotic resistance which includes non-beta-lactam antibiotics as well. Carbapenems are the first-line antibiotics for treatment of such infections.

Bacteria↗

PubMed1985

Fused lacZ genes code for di-, tri- and tetra-beta-galactosidase in Escherichia coli.

Plasmids were constructed which carry two, three or four active lacZ genes of Escherichia coli fused head-to-tail in phase. The products of these oligomeric lacZ genes are shown to be polypeptides with expected subunit mol. wts. of 230 kd (di-beta-galactosidase), 350 kd (tri-beta-galactosidase) and 460 kd (tetra-beta-galactosidase). Di-beta-galactosidase has the same enzymatic activity as the wild-type enzyme. It subunits are practically not degraded proteolytically in vivo. It aggregates predominantly to a dimer which has the same sedimentation constant as the wild-type tetrameric enzyme. Furthermore, it is more heat stable than the wild-type enzyme. Tri- and tetra-beta-galactosidase have strongly reduced enzymatic activities and are largely degraded. Our experiments lead us to propose that covalent joining of two subunits through proper gene duplication may possibly be an intermediate in the evolution of self aggregation of homo-oligomeric proteins.

Electrophoresis, Polyacrylamide Gel↗

PubMed1994

Identification of IS1206, a Corynebacterium glutamicum IS3-related insertion sequence and phylogenetic analysis.

Integration of plasmid pCGL320 into a Corynebacterium glutamicum ATCC21086 derivative led to tandem amplification of the inserted plasmid (Labarre et al., 1993). One amplification event was associated with integration of an insertion sequence that we have named IS1206. Hybridizing sequences were only found in C. glutamicum strains and at various copy numbers. IS1206 is 1290 bp long, carries 32 bp imperfect inverted repeats and generates a 3 bp duplication of the target DNA upon insertion. IS1206 presents the features characteristic of the IS3 family and part of the DNA sequence centering on the putative transposase region (orfB) is similar to those of IS3 and some other related elements. Phylogenetic analysis of orfB deduced protein sequences from IS1206 and IS3-related elements contradicts the phylogeny of the species, suggesting that evolution of these elements might be complex. Horizontal transfer could be invoked but other alternatives like ancestral polymorphism or/and different rates of evolution could also be involved.

Amino Acid Sequence↗

PubMed2002

The function of the nuclear matrix attachment region of silkworm rDNA as an autonomously replicating sequence in plasmid and chromosomal replication origin in yeast.

Nuclear matrix attachment regions (MARs) play a crucial role in chromatin architecture, gene expression, and DNA replication. Although it is well known that yeast autonomously replicating sequences (ARSs) bind nuclear matrix and MARs also function as ARS elements in yeast, whether a heterologous MAR or ARS element acts as a replication origin in the chromosome has not been elucidated. We previously identified a MAR (rMAR) located in the nontranscribed spacer (NTS) of silkworm Attacus ricini rDNA. We report here that this rMAR contains 10 copies of ARS consensus sequence (ACS) and several DNA unwinding regions. The rMAR employs ARS activity in yeast and a rARS element locates in the 3(') region of the rMAR. Furthermore, we have also revealed that either the rMAR or the rARS element functions as a replication origin in the chromosome. Our results provide the first direct evidence to demonstrate that heterologous rMAR and rARS display chromosomal origin activity, suggesting that the chromosome structure and replication origin of rDNA reserve some common features during evolution.

Animals↗

PubMed1998

Molecular characterization of a single mitochondria-associated double-stranded RNA in the green alga Bryopsis.

Mitochondria from the green alga Bryopsis sp. very often contained a 4.5 kb double-stranded RNA (dsRNA) at a defined level. Complementary DNA probes derived from the mitochondrial dsRNA hybridized with none of the algal chloroplast dsRNAs of 1.7 to 2.2 kb, but did hybridize with a similar-sized dsRNA among several dsRNAs from the mitochondria of B. maxima. Sequence analysis of the mitochondrial dsRNA from Bryopsis sp. revealed only two large, overlapping, open reading frames (ORFs) on one strand if UGA was taken as a non-termination codon, suggesting the independent phylogenetic evolution of the mitochondrial dsRNA. Consensus sequence for RNA-dependent RNA polymerase was found within the longer ORF (2472 bp) of the dsRNA. The overlapping 52 bp of the ORFs in different reading frames is suggestive of the occurrence of a -1 ribosomal frameshift in the mitochondrial translation system. The observed simple genetic structures suggest that the algal mitochondrial dsRNA might be deficient in a gene for movement from cell to cell in host plants and, hence, has a plasmid-like nature that is distinct from that of infectious plant viruses. The nature and origin of the endogenous dsRNAs of various sizes and their relationships are discussed.

Amino Acid Sequence↗

PubMed2005

Divided genomes: negotiating the cell cycle in prokaryotes with multiple chromosomes.

Historically, the prokaryotic genome was assumed to consist of a single circular replicon. However, as more microbial genome sequencing projects are completed, it is becoming clear that multipartite genomes comprised of more than one chromosome are not unusual among prokaryotes. Chromosomes are distinguished from plasmids by the presence of essential genes as well as characteristic cell cycle-linked replication kinetics; unlike plasmids, chromosomes initiate replication once per cell cycle. The existence of multipartite prokaryotic genomes raises several questions regarding how multiple chromosomes are replicated and segregated during the cell cycle. These divided genomes also introduce questions regarding chromosome evolution and genome stability. In this review, we discuss these and other issues, with particular emphasis on the cholera pathogen Vibrio cholerae.

Bacteria↗

PubMed1992

The insertion sequence IS200 fingerprints chromosomal genotypes and epidemiological relationships in Salmonella heidelberg.

In Salmonella heidelberg the copy number of the Salmonella-specific insertion element IS200 was found to vary from four to six. All strains tested contained at least one common insertion site which was serovar specific, and most strains contained three common sites. Concurrent analysis of plasmids indicated that all insertion sequence copies were chromosomally located, and also supported the equivalence of an IS200 fingerprint and clonality. Seven intra-serovar clonal lines were thereby identified. One of these was associated with human infections, including septicaemias. Another was associated with chicken as a host: all these strains also carried a unique plasmid of 23 MDa, which was typed as a member of the IncX group. The chromosomal fingerprint of a third clone showed it to be a descendant of the chicken line marked by a single IS200 transposition. One or two representatives of four other clonal lines were identified. These lines of S. heidelberg could be related by divergent evolution, and the most recent relatives conformed to a continuous branching process model of IS200 transposition. This insertion sequence provided a highly discriminatory molecular marker of the S. heidelberg chromosome, and two of the seven clonal lines so identified were associated with distinct clinical/epidemiological contexts.

Animals↗

PubMed2000

Evolution of chloramphenicol resistance, with emergence of cross-resistance to florfenicol, in bovine Salmonella Typhimurium strains implicates definitive phage type (DT) 104.

The prevalence of resistance to florfenicol, a phenicol drug newly introduced in veterinary therapy, was determined in 86 chloramphenicol-resistant Salmonella Typhimurium isolates from cattle collected during 1985-1995. All were highly resistant to chloramphenicol (MICs > or = 128 mg/L) and 38 were simultaneously resistant to florfenicol (MICs >16 mg/L) and to beta-lactam agents, spectinomycin, streptomycin, sulphonamides and tetracyclines. The isolates susceptible to florfenicol harboured the chloramphenicol acetyl transferase gene, cat of type I. All the florfenicol-resistant isolates harboured the floR resistance gene and the characteristic multiple resistance genetic locus, previously characterised in a S. Typhimurium DT104 strain and identified by a multiplex PCR. Plasmid profiles and ribotype patterns were determined for all the isolates. The florfenicol-resistant isolates were grouped into the same ribotyping pattern and presented similar plasmid profiles, whereas the florfenicol-susceptible isolates showed a wider genetic diversity that is usual for S. Typhimurium. Thus, the florfenicol-resistant isolates could represent a clonal cluster, closely related to, if not of DT104 phage type, which appeared in 1989 and is now predominant within chloramphenicol-resistant S. Typhimurium. The multiplex PCR provided a useful tool to survey further evolution of multiresistant S. Typhimurium strains.

Animals↗

PubMed1996

The Garrod Lecture. Evasion of antibiotic action by bacteria.

Antibiotics have reduced the mortality from infectious diseases but not the prevalence of these diseases. Use, and often abuse, of antimicrobial agents encourages the evolution of bacteria toward resistance, often resulting in therapeutic failure. This evolution is due to the emergence of "new' resistance mechanisms and to the spread of well-characterized mechanisms of resistance to the majority of bacterial species. Bacterial resistance can be intrinsic or acquired. Intrinsic resistance is species or genus specific and delineates the spectrum of activity of the antibiotic. Acquired resistance is present in only certain strains of a species or of a genus. The latter results from mutation in a gene located in the host chromosome or a plasmid or from acquisition of new genetic information by a bacterium, mainly by conjugation or transformation. In this review, recent developments in the understanding of biochemical mechanisms and the genetics of resistance is considered for the clinically important antibiotic families.

Anti-Bacterial Agents↗

PubMed1982

Nucleotide sequence definition of a major human repeated DNA, the Hind III 1.9 kb family.

A human Hind III 1.9 kb repeated DNA fragment was isolated and cloned in pBR322. A cloned member that hybridized predominantly to the 1.9 kb Hind III band in a digest of whole human DNA was chosen for sequencing. It is an 1894 bp fragment that shows no significant internal repeats. Few pCG residues are observed in the sequence and there are numerous stop codons. Detailed sequence comparisons confirm this is a novel class of repeats that is not related to previously characterized human satellite DNAs or Alu sequences. At least a portion of the sequence described is conserved in evolution.

Animals↗

PubMed2006

Low abundance of Escherichia coli microsatellites is associated with an extremely low mutation rate.

It is widely assumed that microsatellites are generated by replication slippage, a mutation process specific to repetitive DNA. Consistent with their high mutation rate, microsatellites are highly abundant in most eukaryotic genomes. In Escherichia coli, however, microsatellites are rare and short despite the fact that a high microsatellite mutation rate was described. We show that this high microsatellite instability depends on the presence of the F-plasmid. E. coli cells lacking the F-plasmid have extremely low microsatellite mutation rates. This result provides a possible explanation for the genome-wide low density of microsatellites in E. coli. Furthermore, we show that the F-plasmid induced microsatellite instability is independent of the mismatch repair pathway.

Conjugation, Genetic↗

PubMed2006

Paralogs of genes encoding metal resistance proteins in Cupriavidus metallidurans strain CH34.

Cupriavidus (Wautersia, Ralstonia, Alcaligenes) metallidurans strain CH34is a well-studied example of a metal-resistant proteobacterium. Genome sequence analysis revealed the presence of a variety of paralogs of proteins that were previously shown to be involved in heavy metal resistance. Which advantage has C. metallidurans in maintaining all these paralogs during evolution? Paralogs investigated belong to the families RND (resistance nodulation cell division) or CHR (chromate resistance). The respective genes were localized by PCR either on one of the two native megaplasmids pMOL28 and pMOL30 of strain CH34, or on its chromosomal DNA. Gene expression was studied by real-time reverse transcriptase PCR and by reporter gene constructs. Genes found to be inducible were disrupted and their contribution to metal resistance measured. When two or three highly related genes were present, usually one was inducible by heavy metals while the other one or two were silent or constitutively expressed. This suggests that C. metallidurans CH34 carries a variety of no longer or not yet used genes that might serve as surplus material for further developments, an advantage that may compensate for the costs of maintaining these genes during evolution.

Bacterial Proteins↗