The use of an improved transposon mutagenesis system for DNA sequencing leads to the characterization of a new insertion sequence of Streptomyces lividans 66

Evolution of melanocortin receptors in teleost fish: The melanocortin type 1 receptor

The melanocortin type 1 receptor (Mc1r) belongs to a family of G-protein-coupled receptors involved in various physiological processes in vertebrates. Melanocortins, the Mcr natural agonists, are pituitary peptide hormones including adrenocorticotropin and melanocyte-stimulating hormones. In mammals and birds, Mc1r is involved in pigmentation and expressed in melanocytes and melanoma. Activation of Mc1r leads to eumelanin production as well as to proliferation and survival of melanocytes in the epidermis. Here we report the molecular and evolutionary analysis of mc1r from three major fish models, the zebrafish Danio rerio, the medaka Oryzias latipes and the platyfish Xiphophorus maculatus. In contrast to some other melanocortin receptor genes, mc1r has been conserved as a single copy gene in divergent fish species. Its expression was detected in all organs tested in platyfish and medaka but was restricted to eyes, skin, brain and testis in zebrafish, this possibly reflecting differences in the distribution of extracutaneous melanophores. The mc1r gene was found to be expressed during embryogenesis, as well as in Xiphophorus hybrid melanoma, similar to human tumours. Protein sequence comparison between fish and mammalian Mc1r revealed a remarkable concordance between evolutionary and functional analyses for the identification of residues and regions critical for receptor function.

Cloning of the netropsin resistance genes from Streptomyces flavopersicus NRRL 2820

Streptomyces flavopersicus NRRL 2820 (synonym: Streptomyces netropsis DSM40093) is resistant to the N-methylpyrrole-containing oligopeptide antibiotic netropsin. A 9.38 kb DNA-fragment was isolated from a genomic library of Streptomyces flavopersicus using an Escherichia coli-Streptomyces lividans shuttle vector which enables S. lividans to grow on netropsin-containing agar plates. By subcloning, the resistance was conferred to a 5.9 kb Eco RV fragment. DNA sequence analysis of this Eco RV fragment revealed two open reading frames (netP1 , 1556 bp and netP2 , 1773 bp). The deduced proteins share significant similarity to each other (27% identity) and to the large family to ABC-type multidrug resistance proteins. In each protein a conserved transmembrane and ATP binding domain was identified. Deletion analysis showed that both proteins are necessary for netropsin resistance indicating that the proteins form a heterodimeric ABC-transporter exporting netropsin.

Identification of the -1 translational frameshift sites using a liquid chromatography-tandem mass spectrometric approach

Translational frameshifting, a ubiquitous mechanism used to produce alternative proteins for different biological purposes, appears in a variety of genes in probably all organisms. In the past, the combinational use of sophisticated expression vectors, specific endopeptidases, and Edman degradation has been the main approach for identification of the translational frameshift sites. Although Edman degradation is highly reliable, it is also time-consuming and costly. In this article, we report a new liquid chromatography-tandem mass spectrometric (LC-MS/MS) approach for identifying the -1 translational frameshift sites. The approach consists of three steps: (i) LC-MS/MS analysis of the protein digests, (ii) primary data analysis using the known mRNA sequence, and (iii) advanced data analysis using a new database containing distinct mRNA sequences with single insertion at particular positions. We first validated our approach by analyzing the previously documented slippery sequence, A4G, from IS3. With this approach, we further determined whether the TTTTTTG (T6G) sequence of IS1372 from Streptomyces lividans had the -1 translational frameshifting potential. The identified amino acid sequence of the transframe peptide indicated that the -1 frameshifting occurred at the T6G motif, as predicted previously. The results on IS3 (A4G) and IS1372 (T6G) suggested that this approach is effective for the translational frameshifting studies.

Cloning of the dmrt1 gene of Xiphophorus maculatus: dmY/dmrt1Y is not the master sex-determining gene in the platyfish

In contrast to the situation observed in mammals and birds, a switching between different sex determination systems frequently occurred during the evolution of the teleost fish lineage. This might be due to a frequent turnover of sex-determining signals at the top of the sex determination cascade (master sex-determining genes in the case of genetic sex determination). Alternatively, different variations of a same master gene might decide the sex of individuals in different sex determination systems. In the medaka Oryzias latipes, a Y-specific copy of the putative transcription factor gene dmrt1 very likely corresponds to the master sex-determining gene inducing male formation [Nature 417 (2002) 559; Proc. Natl. Acad. Sci. U. S. A. 99 (2002) 11778]. This gene, alternately called dmY and dmrt1Y, has been formed by duplication of the autosomal dmrt1. In order to determine if an orthologue of dmrt1Y was also located in the sex determination region of the related platyfish Xiphophorus maculatus, Southern blot analysis was performed on genomic DNA from XY and YY males and WY and XX females using both medaka and human dmrt1 cDNA as probes. Using different restriction enzymes, no evidence for sex-specific dmrt-containing genomic fragments could be found in the platyfish. No dmrt gene could be detected by low-stringency Southern blot analysis of genomic inserts from 60 bacterial artificial chromosome (BAC) clones linked to the sex-determining locus on the X and Y chromosomes. Six different groups of BAC clones containing dmrt genes were isolated from a platyfish genomic library. X. maculatus dmrt1 gene and cDNA were characterised. In adult, expression of dmrt1 was detected only in testis. Phylogenetic analysis indicated that the duplication of dmrt1 that led to the formation of dmY/dmrt1Y within the medaka lineage clearly occurred after its divergence from the platyfish lineage. Hence, a dmY/dmrt1Y orthologue generated by this particular event of duplication does not correspond to the master sex-determining gene in the platyfish.

The xmrk oncogene can escape nonfunctionalization in a highly unstable subtelomeric region of the genome of the fish xiphophorus☆

The Xmrk oncogene involved in melanoma formation in the fish Xiphophorus was formed relatively recently by duplication of the epidermal growth factor co-orthologue egfrb. In the platyfish X. maculatus, Xmrk is located close to the major sex-determining locus in a subtelomeric region of the X and Y sex chromosomes that frequently undergoes duplications and other rearrangements. This region accumulates repetitive sequences: more than 80% of the 33-kb region 3' of Xmrk is constituted by retrotransposable elements. The high degree of nucleotide identity between X- and Y-linked sequences and the rarity of gonosome-specific rearrangements indicated that the instability observed was not a manifestation of gonosome-specific degeneration. Seven other duplicated genes were found, all corresponding, in contrast to Xmrk, to pseudogenes (nonfunctionalization). Functional persistence of Xmrk in a highly unstable region in divergent Xiphophorus species suggests a beneficial function under certain conditions for this dispensable and potentially injurious gene.

Streptomyces coelicolor A3(2) plasmid SCP2*: deductions from the complete sequence

Plasmid SCP2* is a 31 kb, circular, low-copy-number plasmid originally identified in Streptomyces coelicolor A3(2) as a fertility factor. The plasmid was completely sequenced. The analysis of the 31 317 bp sequence revealed 34 ORFs encoding putative proteins from 31 to 710 aa long, most of them lacking similarity to known proteins. Three functional regions had been identified previously: the replication region, the transfer and spreading region, and the stability region. Three genes were identified in the stability region which contribute to the stability of SCP2 as shown by plasmid stability testing. The first gene, mrpA, encodes a new member of the lambda integrase family of site-specific recombinases. The two genes downstream of mrpA were called parA and parB. The gene product, ParA, shows similarity to a family of ATPases involved in plasmid partition. An increase of plasmid stability could be seen only when both genes were present. By deletion analysis, the replication region could be narrowed down to a 1.6 kb region, consisting of a 650 bp non-coding region and two genes, repI and repII, encoding proteins of 161 and 131 aa. Only RepI exhibits similarities to DNA binding elements and contains a putative helix-turn-helix motif. The traA gene that is essential for DNA transfer and pock formation was identified previously. Upstream of traA, 10 ORFs were found in the same orientation as traA which might be involved in conjugation and DNA spreading, together with one gene in the opposite orientation with similarities to transcriptional regulators of DNA transfer. Two transposable elements were found on SCP2*. IS1648 belongs to the IS3 family of insertion sequences. The second element, Tn5417, shows the highest similarity to the Tn4811 element located in the terminal inverted repeats of the Streptomyces lividans chromosome.

Once the circle has been broken: dynamics and evolution of Streptomyces chromosomes

Chromosomal instability has been a hallmark of Streptomyces genetics. Deletions and circularization often occur in the less-conserved terminal sequences of the linear chromosomes, which contain swarms of transposable elements and other horizontally transferred elements. Intermolecular recombination involving these regions also generates gross exchanges, resulting in terminal inverted repeats of heterogeneous size and context. The structural instability is evidently related to evolution of the Streptomyces chromosomes, which is postulated to involve linearization of hypothetical circular progenitors via integration of a linear plasmid. This scenario is supported by several bioinformatic analyses.

Molecular cloning and characterization of DMRT genes from the medaka Oryzias latipes and the platyfish Xiphophorus maculatus

The DMRT genes constitute a family of genes, which possess a common motif called the DM domain. DMRT1 is considered to be involved in sex determination and/or sex differentiation, but not much information exists about the function of the other gene family members. We cloned DMRT genes of two important model fish species, the medaka, Oryzias latipes, and the platyfish, Xiphophorus maculatus. Based on sequence similarity and genomic structure with known DMRT genes, the gene from the medaka was identified as OlaDMRT4, and those from the platyfish as XmaDMRT2 and XmaDMRT4. OlaDMRT4 was assigned to the linkage group 18 (LG18) of the medaka by linkage analysis and fluorescence in situ hybridization. The earlier cloned medaka DMRT1, 2 and 3 genes form a cluster on LG9. Therefore, OlaDMRT4 does not belong to the DMRT gene cluster. In adult medaka fish, OlaDMRT4 is expressed in the brain, eyes, gill, kidney, as well as testis and ovary. During development, OlaDMRT4 exists as maternal transcripts, and is expressed until early larval stages. This pattern of expression differs from the other known medaka DMRT genes. Surprisingly it is also not the same as its putative tilapia ortholog (DMO). These differences in expression suggest that DMRT4 might fulfill divergent functions in different species.

Construction and initial analysis of bacterial artificial chromosome (BAC) contigs from the sex-determining region of the platyfish Xiphophorus maculatus

Despite the major importance of sex determination in aquaculture, no master sex-determining gene has been identified so far in teleost fish. In the platyfish Xiphophorus maculatus, this master gene is flanked by two receptor tyrosine kinase genes, the Xmrk oncogene responsible for melanoma formation in some Xiphophorus interspecific hybrids, and its proto-oncogenic counterpart. Both Xmrk genes, which have already been characterised at the molecular level, delimit a region of about 1 Mb that contains other gene loci involved in sexual maturity, pigmentation and melanoma formation. We have constructed a genomic bacterial artificial chromosome (BAC) library of X. maculatus with a tenfold coverage of the haploid genome and walked on both X and Y sex chromosomes starting from both Xmrk genes. This led to the assembly of BAC contigs from the sex-determining region covering approximately 950 kb of the X and 750 kb of the Y chromosome. To our knowledge, these are the largest contigs reported so far for sex chromosomes in fish. Molecular analysis suggests that the sex-determining region of X. maculatus frequently undergoes retrotranspositions and other kinds of rearrangements. This genomic plasticity might be related to the high genetic variability observed in Xiphophorus for sex determination, sexual maturity, pigmentation and melanoma formation, which are encoded by gene loci located in the sex-determining region.

Jule from the fish Xiphophorus is the first complete vertebrate Ty3/Gypsy retrotransposon from the Mag family

Jule is the second complete long-terminal-repeat (LTR) Ty3/Gypsy retrotransposon identified to date in vertebrates. Jule, first isolated from the poeciliid fish Xiphophorus maculatus, is 4.8 kb in length, is flanked by two 202-bp LTRs, and encodes Gag (structural core protein) and Pol (protease, reverse transcriptase, RNase H, and integrase, in that order) but no envelope. There are three to four copies of Jule per haploid genome in X. maculatus. Two of them are located in a subtelomeric region of the sex chromosomes, where they are associated with the Xmrk receptor tyrosine kinase genes, of which oncogenic versions are responsible for the formation of hereditary melanoma in Xiphophorus. One almost intact copy of Jule was found in the first intron of the X-chromosomal allele of the Xmrk proto-oncogene, and a second, more corrupted copy is present only 56 nt downstream of the polyadenylation signal of the Xmrk oncogene. Jule-related elements were detected by Southern blot hybridization with less than 10 copies per haploid genome in numerous other poeciliids, as well as in more divergent fishes, including the medakafish Oryzias latipes and the tilapia Oreochromis niloticus. Database searches also identified Jule-related sequences in the zebrafish Danio rerio and in both genome project pufferfishes, Fugu rubripes and Tetraodon nigroviridis. Phylogenetic analysis revealed that Jule is the first member of the Mag family of Ty3/Gypsy retrotransposons described to date in vertebrates. This family includes the silkworm Mag and sea urchin SURL retrotransposons, as well as sequences from the nematode Caenorhabditis elegans. Additional related elements were identified in the genomes of the malaria mosquito Anopheles gambiae and the nematode Ascaris lumbricoides. Phylogeny of Mag-related elements suggested that the Mag family of retrotransposons is polyphyletic and is constituted of several ancient lineages that diverged before their host genomes more than 600 MYA.

Identification and typing of Streptomyces strains: evaluation of interspecific, intraspecific and intraclonal differences by RAPD fingerprinting

The suitability of random amplified polymorphic DNA PCR for the detection of differences between Streptomyces species and strains was evaluated. For this purpose, a protocol of RAPD specific for Streptomyces DNA, i.e. suitable for DNA presenting a high G+C content, was developed using S. ambofaciens ATCC23877. Among the 30 primers tested, all containing 80% G+C, 17 gave a pattern with this strain. Six oligonucleotides were chosen to compare 12 strains belonging to six species of Streptomyces. These oligonucleotides were then used to determine whether these strains could be differentiated at the DNA level with this method. All fingerprints obtained with six primers differed from one species to another. We showed that the RAPD method could be used to reveal intraspecific and intraclonal polymorphisms. Thus, RAPD allows for the rapid, sensitive and specific detection of genetic diversity among species and strains of Streptomyces.

Multiple lineages of the non-LTR retrotransposon Rex1 with varying success in invading fish genomes

Rex1, together with the related BABAR: elements, represents a new family of non-long-terminal-repeat (non-LTR) retrotransposons from fish, which might be related to the CR1 clade of LINE elements. Rex1/BABAR: retrotransposons encode a reverse transcriptase and an apurinic/apyrimidinic endonuclease, which is very frequently removed by incomplete reverse transcription. Different Rex1 elements show a conserved terminal 3' untranslated region followed by oligonucleotide tandem repeats of variable size and sequence. Phylogenetic analysis revealed that Rex1 retrotransposons were frequently active during fish evolution. They formed multiple ancient lineages, which underwent several independent and recent bursts of retrotransposition and invaded fish genomes with varying success (from <5 to 500 copies per haploid genome). At least three of these ancient Rex1 lineages were detected within the genome of poeciliids. One lineage is absent from some poeciliids but underwent successive rounds of retrotransposition in others, thereby increasing its copy number from <10 to about 200. At least three ancient Rex1 lineages were also detected in the genome project fish Fugu rubripes. Rex1 distribution within one of its major lineages is discontinuous: Rex1 was found in all Acanthopterygii (common ancestor in the main teleost lineage approximately 90 MYA) and in both European and Japanese eels (divergence from the main teleost lineage about 180 MYA) but not in trout, pike, carp, and zebrafish (divergence 100-120 MYA). This might either result from frequent loss or rapid divergence of Rex1 elements specifically in some fish lineages or represent one of the very rare examples of horizontal transfer of non-LTR retrotransposons. This analysis highlights the dynamics and complexity of retrotransposon evolution and the variability of the impact of retrotransposons on vertebrate genomes.

Genetic instability associated with insertion of IS6100 into one end of the Streptomyces lividans chromosome

Analysis of 548 recombinant strains of Streptomyces lividans carrying chromosomal insertions of IS6100 revealed that six mutants contained DNA amplifications. The amplifications differed in size but included IS6100 sequences. Hybridization with representative cosmid clones containing sequences from the unstable regions of the chromosome indicated that, in each mutant, DNA rearrangements affected just one of the chromosome ends. The amplifications were derived either from a region immediately proximal to the terminal inverted repeat (TIR) or further distal, from a previously characterized type I amplifiable unit of DNA. There was no evidence for extensive deletions accompanying the amplifications and chromosome linearity was maintained with, at least in five mutants, clear evidence for no loss of either TIR. The nature of the rearrangements provides evidence that insertions affecting the integrity of a chromosome end can contribute to genetic instability in Streptomyces.

The mannitol utilization genes of Pseudomonas fluorescens are regulated by an activator: cloning, nucleotide sequence and expression of the mtlR gene

A plasmid with the galK gene under control of the promoter of the mannitol utilization genes (mtl) from Pseudomonas fluorescens DSM 50106 was constructed to isolate the mtl regulatory gene. An Escherichia coli galK- mtl- strain with this plasmid was used to screen a genomic library of P. fluorescens for the presence of the regulatory gene by plating on McConkey agar plates supplemented with galactose and mannitol. Clones carrying the regulatory gene were isolated and by complemention assays, deletion analysis and DNA sequencing an open reading frame (mtlR) of 906nt identified encoding the regulator. The deduced protein MtlR with a calculated molecular mass of 34.7kDa showed a low overall similarity to several other regulatory proteins of the XylS/AraC family. When mtlR was cloned and expressed in E. coli, the protein was produced as inclusion bodies. Complete denaturation followed by subsequent slow refolding led to low amounts of active protein. The activity was shown in gel mobility shift assays by binding of MtlR to a DNA fragment containing the promoter/operator region of the P. fluorescens mtl genes.

The telomeres of Streptomyces chromosomes contain conserved palindromic sequences with potential to form complex secondary structures

The chromosomes of the gram-positive soil bacteria Streptomyces are linear DNA molecules, usually of about 8Mb, containing a centrally located origin of replication and covalently bound terminal proteins (which are presumably involved in the completion of replication of the telomeres). The ends of the chromosomes contain inverted repeats of variable lengths. The terminal segments of five Streptomyces chromosomes and plasmids were cloned and sequenced. The sequences showed a high degree of conservation in the first 166-168bp. Beyond the terminal homology, the sequences diverged and did not generally cross-hybridize. The homologous regions contained seven palindromes with a few nucleotide differences. Many of these differences occur in complementary pairs, such that the palindromicity is preserved. Energy-optimized modelling predicted that the 3' strand of the terminal palindromes can form extensive hairpin structures that are similar to the 3' ends of autonomous parvovirus genomes. Most of the putative hairpins have a GCGCAGC sequence at the loop, with the potential to form a stable single C-residue loop closed by a sheared G:A pairing. The similarity between the terminal structures of the Streptomyces replicons and the autonomous parvoviral genomes suggests that they may share some structural and/or replication features.

Use of a transposon-encoded site-specific resolution system for construction of large and defined deletion mutations in bacterial chromosome

A class II transposon, Tn1722, encodes a site-specific resolution system, in which the resolvase (TnpR) efficiently catalyzes intramolecular recombination between the two directly oriented copies of the resolution site (res), leading to precise excision of the intervening DNA region. This property was exploited to develop the general strategies to introduce the large and defined deletion mutations into the bacterial chromosome. The Tn1722 res site was inserted into the plasmid carrying a cloned chromosomal fragment, and the resulting plasmid was integrated into a Tn1722-containing target chromosome by single crossover-mediated homologous recombination. The plasmid integrant carrying the two copies of the res site in the same orientation could efficiently excise the chromosomal region locating between the two res sites by means of the site-specific resolution system. Such site-specific deletion could be also detected by appropriate integration of the res-tnpR-containing plasmid into the chromosome in which another copy of the res site had been inserted through allelic exchange. This latter strategy was further modified to isolate the deletion mutations that were free of the resistance markers used for introduction of the res site and the res-tnpR block into the target chromosome. The deletion systems were applied to analyze the 103-kb pvd region of Pseudomonas aeruginosa PAO carrying most of the pyoverdin biosynthetic genes. Successful isolation of the mutation lacking more than a 100-kb fragment in the pvd region indicated that this region did not carry any essential genes.

Structure and function of the genes involved in mannitol, arabitol and glucitol utilization from Pseudomonas fluorescens DSM50106

A DNA fragment from Pseudomonas fluorescens DSM50106 containing the genes for the uptake and utilization of mannitol, arabitol and glucitol was cloned in Escherichia coli and sequenced. Seven open reading frames (mtlEFGKDYZ) were identified on the 10031 bp fragment. The deduced amino acid sequences of the first four open reading frames (mtlEFGK) revealed significant similarity to the components of the maltose transport system in E. coli and Salmonella typhimurium. The gene mtlD encoding a polyol dehydrogenase was located downstream of mtlK. The deduced proteins of the last two genes on the fragment showed a high similarity to a fructokinase from Vibrio alginolyticus (MtlZ) and a xylulose kinase from Streptomyces rubiginosus (MtlY), respectively. Both genes were expressed in E. coli. MtlZ phosphorylated fructose, glucose and glucitol whereas MtlY was highly specific for xylulose. Upstream of mtlE, a putative promoter/operator region was identified by promoter probe studies which was active in P. fluorescens but not in E. coli.

Genetic instability of the Streptomyces chromosome

The Streptomyces wild-type chromosome is linear in all examples studied. The ends of the chromosome or telomeres consist of terminal inverted repeats of various sizes with proteins covalently bound to their 5' ends. The chromosome is very unstable and undergoes very large deletions spontaneously at rates higher than 0.1% of spores. Frequently, the telomeres are included in the deletions. Loss of both telomeres leads to circularization of the chromosome. The wild-type chromosome can also be circularized artificially by targeted recombination. Spontaneously or artificially circularized chromosomes are even more unstable than the linear ones. High-copy-number tandem amplifications of specific chromosomal regions are frequently associated with the deletions. RecA seems to be involved in the amplification mechanism and control of genetic instability.