[Show abstract][Hide abstract] ABSTRACT: Linear chromosomes and linear plasmids of Streptomyces are capped by terminal proteins that are covalently bound to the 5'-ends of DNA. Replication is initiated from an internal origin, which leaves single-stranded gaps at the 3'-ends. These gaps are patched by terminal protein-primed DNA synthesis. Streptomyces contain five DNA polymerases: one DNA polymerase I (Pol I), two DNA polymerases III (Pol III) and two DNA polymerases IV (Pol IV). Of these, one Pol III, DnaE1, is essential for replication, and Pol I is not required for end patching. In this study, we found the two Pol IVs (DinB1 and DinB2) to be involved in end patching. dinB1 and dinB2 could not be co-deleted from wild-type strains containing a linear chromosome, but could be co-deleted from mutant strains containing a circular chromosome. The resulting ΔdinB1 ΔdinB2 mutants supported replication of circular but not linear plasmids, and exhibited increased ultraviolet sensitivity and ultraviolet-induced mutagenesis. In contrast, the second Pol III, DnaE2, was not required for replication, end patching, or ultraviolet resistance and mutagenesis. All five polymerase genes are relatively syntenous in the Streptomyces chromosomes, including a 4-bp overlap between dnaE2 and dinB2. Phylogenetic analysis showed that the dinB1-dinB2 duplication occurred in a common actinobacterial ancestor.
Nucleic Acids Research 02/2012; 40(3):1118-30. DOI:10.1093/nar/gkr856 · 9.11 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The present study focuses on schizophrenia patient subgroups with specific symptom pattern using the Positive and Negative Syndrome Scale (PANSS). In this report, we intend to (1) provide a more appropriate analytic method for exploring the subgroups based on PANSS data, (2) validate identified subgroups with external variables, and (3) estimate probabilities of subgroup changes between 2 disease states. The analyzed data include 219 acute-state patients who had completed the PANSS within 1 week of index admission and 225 subsided-state patients who were living in the community and under family care. Regression extension of latent class analysis was performed. We found that acute schizophrenia can be classified into 4 subgroups--whole syndrome, whole syndrome without hostility, partial syndrome with negative symptoms, and partial syndrome with pure reality distortion--and that subsided schizophrenia can be classified into 3 subgroups--florid symptom, marked negative, and remitted. Patients of the whole syndrome, whole syndrome without hostility, partial syndrome with negative symptoms, and partial syndrome with pure reality distortion subgroups at the acute state were most likely to transit to the florid symptom (61%), florid symptom (48%), marked negative (42%), and remitted (56%) subgroups at the subsided state, respectively. Significant relationships of obtained subgroups with sociodemographic variables and neurocognitive variables were identified. These results of different subgroups will provide the background for facilitating current molecular, genetic, and neurobiological studies of schizophrenia.
[Show abstract][Hide abstract] ABSTRACT: Linear chromosomes and linear plasmids of Streptomyces possess covalently bound terminal proteins (TPs) at the 5' ends of their telomeres. These TPs are proposed to act as primers for DNA synthesis that patches the single-stranded gaps at the 3' ends during replication. Most ('archetypal') Streptomyces TPs (designated Tpg) are highly conserved in size and sequence. In addition, there are a number of atypical TPs with heterologous sequences and sizes, one of which is Tpc that caps SCP1 plasmid of Streptomyces coelicolor. Interactions between the TPs on the linear Streptomyces replicons have been suggested by electrophoretic behaviors of TP-capped DNA and circular genetic maps of Streptomyces chromosomes. Using chemical cross-linking, we demonstrated intramolecular and intermolecular interactions in vivo between Tpgs, between Tpcs and between Tpg and Tpc. Interactions between the chromosomal and plasmid telomeres were also detected in vivo. The intramolecular telomere interactions produced negative superhelicity in the linear DNA, which was relaxed by topoisomerase I. Such intramolecular association between the TPs poses a post-replicational complication in the formation of a pseudo-dimeric structure that requires resolution by exchanging TPs or DNA.
Nucleic Acids Research 11/2010; 39(6):2165-74. DOI:10.1093/nar/gkq1204 · 9.11 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Bidirectional replication of the linear chromosomes and plasmids of Streptomyces spp. results in single-strand overhangs at their 3' ends, which contain extensive complex palindromic sequences. The overhangs are believed to be patched by DNA synthesis primed by a terminal protein that remains covalently bound to the 5' ends of the telomeres. We discovered that in vitro a conserved 167-bp telomere DNA binds strongly to RNA polymerase holoenzyme and exhibits promoter activities stronger than those of an rRNA operon. In vivo, the telomere DNA exhibited promoter activity in both orientations on a circular plasmid in Streptomyces. The telomere promoter is also active on a linear plasmid during exponential growth. Such promoter activity in a telomere has not hitherto been observed in eukaryotic or prokaryotic replicons. Streptomyces telomere promoters may be involved in priming the terminal Okazaki fragment (during replication) replicative transfer (during conjugation), or expression of downstream genes (including a conserved ttrA helicase-like gene involved in conjugal transfer). Interestingly, the Streptomyces telomeres also function as a promoter in Escherichia coli and as a transcription enhancer in yeast.
Journal of bacteriology 02/2009; 191(3):773-81. DOI:10.1128/JB.01299-08 · 2.81 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: We observed a spontaneous amplification of the Streptomyces coelicolor chromosome, including genes encoding biosynthetic enzymes of the antibiotic actinorhodin. A new junction of two tandem segments
has, inserted within it, a third copy of a transposable element existing in two places elsewhere in the chromosome, suggesting
its involvement in the amplification mechanism.
Journal of bacteriology 08/2008; 190(13):4754-8. DOI:10.1128/JB.00131-08 · 2.81 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Streptomyces species are highly abundant soil bacteria that possess linear chromosomes (and linear plasmids). The 5' ends of these molecules are covalently bound by terminal proteins (TPs), that are important for integrity and replication of the telomeres. There are at least two types of TPs, both of which contain a DNA-binding domain and a classical eukaryotic nuclear localization signal (NLS). Here we show that the NLS motifs on these TPs are highly efficient in targeting the proteins along with covalently bound plasmid DNA into the nuclei of human cells. The TP-mediated nuclear targeting resembles the inter-kingdom gene transfer mediated by Ti plasmids of Agrobacterium tumefaciens, in which a piece of the Ti plasmid DNA is targeted to the plant nuclei by a covalently bound NLS-containing protein. The discovery of the nuclear localization functions of the Streptomyces TPs not only suggests possible inter-kingdom gene exchanges between Streptomyces and eukaryotes in soil but also provides a novel strategy for gene delivery in humans and other eukaryotes.
Nucleic Acids Research 07/2008; 36(10):e62. DOI:10.1093/nar/gkm1170 · 9.11 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: We report a previously unobserved form of genetic instability for Streptomyces coelicolor, the replacement of one chromosome end by the other end. These genetic changes occurred spontaneously in both a wild-type
strain and strains harboring a foreign transposon. Deleted and duplicated DNA comprises up to 33% of the genome.
Journal of bacteriology 01/2008; 189(24):9117-21. DOI:10.1128/JB.01049-07 · 2.81 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Linear plasmids and chromosomes of Streptomyces carry terminal proteins (TPs) covalently attached to the 5' ends of the DNA. Most known telomeres are conserved in primary sequence and in the potential secondary structures formed during replication. The TP that caps these telomeres is also highly conserved and its coding gene, tpg, is present in all Streptomyces chromosomes and some linear plasmids. Linear plasmid SCP1 contains atypical telomere sequences and no tpg homologue, and can replicate in the absence of tpg, suggesting that it carries a novel TP gene. To isolate the TP on the SCP1 telomeres, we constructed a multicopy mini-SCP1 plasmid. The TP capping the plasmid was isolated and subjected to tryptic digestion and mass spectrometric analysis, and the results indicated that the TP was encoded by an open reading frame (ORF), SCP1.127 (tpc), on SCP1. Of the two ORFs upstream of tpc, SCP1.125 (tac) but not SCP1.126 was essential for replication of mini-SCP1. The Tac-Tpc system of SCP1 represents a convergently evolved novel telomere-capping system of Streptomyces linear replicons.
[Show abstract][Hide abstract] ABSTRACT: Single-stranded gaps at the 3′ ends of Streptomyces linear replicons are patched by DNA synthesis primed by terminal proteins (TP) during replication. We devised an in vitro
system that specifically incorporated dCMP, the first nucleotide at the 5′ ends, onto a threonine residue of the TP of Streptomyces coelicolor.
[Show abstract][Hide abstract] ABSTRACT: SLP2 is a 50 kb linear plasmid in Streptomyces lividans that contains short (44 bp) terminal inverted repeats and covalently bound terminal proteins. The nucleotide sequence of SLP2 was determined. The rightmost 15.4 kb sequence is identical to that of the host chromosome, including the Tn4811 sequence at the border, which is interrupted by an insertion sequence (IS) element in SLP2. Examination of the flanking target sequences of Tn4811 suggests a previous recombinational event there. The 43 putative protein coding sequences contained many involved in replication (including two terminal protein homologues), partitioning, conjugal transfer and intramycelial spread. The terminally located helicase-like gene ttrA was necessary for conjugal transfer. The two telomeres diverge significantly in primary sequence, while preserving similar secondary structures. Mini-linear plasmids containing these telomeres replicated in S. lividans using the chromosomally encoded terminal protein. In addition, two pseudotelomere sequences are present near the left telomere. The G+C content and GC or AT skew profiles exhibit complex distributions. These, plus the inferred recombination at the right arm, indicate that SLP2 has evolved through rounds of exchanges involving at least three replicons.
[Show abstract][Hide abstract] ABSTRACT: 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.
Trends in Genetics 11/2002; 18(10):522-9. DOI:10.1016/S0168-9525(02)02752-X · 9.92 Impact Factor