A simplified and reliable protocol for plasmid DNA sequencing: fast miniprep and denaturation

Platon: identification and characterization of bacterial plasmid contigs in short-read draft assemblies exploiting protein sequence-based replicon distribution scores

Plasmids are extrachromosomal genetic elements that replicate independently of the chromosome and play a vital role in the environmental adaptation of bacteria. Due to potential mobilization or conjugation capabilities, plasmids are important genetic vehicles for antimicrobial resistance genes and virulence factors with huge and increasing clinical implications. They are therefore subject to large genomic studies within the scientific community worldwide. As a result of rapidly improving next-generation sequencing methods, the quantity of sequenced bacterial genomes is constantly increasing, in turn raising the need for specialized tools to (i) extract plasmid sequences from draft assemblies, (ii) derive their origin and distribution, and (iii) further investigate their genetic repertoire. Recently, several bioinformatic methods and tools have emerged to tackle this issue; however, a combination of high sensitivity and specificity in plasmid sequence identification is rarely achieved in a taxon-independent manner. In addition, many software tools are not appropriate for large high-throughput analyses or cannot be included in existing software pipelines due to their technical design or software implementation. In this study, we investigated differences in the replicon distributions of protein-coding genes on a large scale as a new approach to distinguish plasmid-borne from chromosome-borne contigs. We defined and computed statistical discrimination thresholds for a new metric: the replicon distribution score (RDS), which achieved an accuracy of 96.6 %. The final performance was further improved by the combination of the RDS metric with heuristics exploiting several plasmid-specific higher-level contig characterizations. We implemented this workflow in a new high-throughput taxon-independent bioinformatics software tool called Platon for the recruitment and characterization of plasmid-borne contigs from short-read draft assemblies. Compared to PlasFlow, Platon achieved a higher accuracy (97.5 %) and more balanced predictions (F1=82.6 %) tested on a broad range of bacterial taxa and better or equal performance against the targeted tools PlasmidFinder and PlaScope on sequenced Escherichia coli isolates. Platon is available at: http://platon.computational.bio/.

Optimization of protocol for sequencing of difficult templates

In this paper, we have fine-tuned a DNA sequencing protocol suitable for a wide range of difficult templates. The primary goal was to evaluate a number of parameters--such as various dye terminator mixes in the presence or absence of additives, the amount of DNA or primer, and cycling protocols--about the effectiveness of reading through complex regions. We showed that the modification of a published protocol leads to significant (75%) cost reduction without forfeiting quality of the data. In the recommended protocol, we used betaine as a standard additive, but better results can be obtained when betaine and Reagent A are mixed in an equivalent ratio.

Fundamentals of sequencing of difficult templates--an overview

Despite enormous progress, the DNA sequencing of difficult regions, whether they are part of complex genomes or individual constructs, still presents a significant challenge and may require many trials, brute-force, or the intervention of a very experienced sequencer (and sometimes all of the above). Very early on, it was realized that sequencing of various types of difficult templates requires distinct treatments. To sequence through GC-rich regions, the addition of DMSO, NP-40/Tween-20 detergents, or the mix (4:1) of BD3.0:dGTP3.0 was sometimes helpful. To get through long poly-A/T tails, sometimes one would be successful using tailored poly- A/T (V/B) N primers or primers that spanned part of pre-tail and tail regions. A few years ago invitrogen introduced a set of sequencing additives that proved to be useful for many different types of difficult templates.

Multiplexed automated DNA sequencing directly from single bacterial colonies

Sample preparation has been one of the major bottlenecks for large-scale DNA sequencing projects in terms of time and cost. To improve sample throughput and to integrate the front-end tasks to capillary-array DNA sequencers, protocols for directly sequencing the plasmids from a single bacterial colony in fused-silica capillaries were developed. After the colony is picked, lysis is accomplished in situ in the plastic sample tube using either a thermocycler or a heating block. Upon heating, the plasmids are released while chromosomal DNA and membrane proteins are denatured and precipitate to the bottom of the tube. After adding enzyme and Sanger reagents, the resulting solution was aspirated into the reaction capillaries by a syringe pump, and cycle sequencing was initiated. No deleterious effect upon the reaction efficiency, the on-line purification system, or the capillary electrophoresis separation was observed, even though the crude lysate was used as the template. Multiplexed online DNA sequencing data from 8 parallel channels allowed base calling up to 620 bp with an accuracy of 98%. The entire system can be automatically regenerated for repeated operation. By the marriage of colony sequencing with the capillary array sequencer, both the front end and the back end of DNA sequencing are combined in a miniaturized format. This protocol will ultimately reduce the cost of sequencing to well below current levels.

Sequences and expression of pyruvate dehydrogenase genes from Pseudomonas aeruginosa

A mutant of Pseudomonas aeruginosa, OT2100, which appeared to be defective in the production of the fluorescent yellow-green siderophore pyoverdine had been isolated previously following transposon mutagenesis (T. R. Merriman and I. L. Lamont, Gene 126:17-23, 1993). DNA from either side of the transposon insertion site was cloned, and the sequence was determined. The mutated gene had strong identity with the dihydrolipoamide acetyltransferase (E2) components of pyruvate dehydrogenase (PDH) from other bacterial species. Enzyme assays revealed that the mutant was defective in the E2 subunit of PDH, preventing assembly of a functional complex. PDH activity in OT2100 cell extracts was restored when extract from an E1 mutant was added. On the basis of this evidence, OT2100 was identified as an aceB or E2 mutant. A second gene, aceA, which is likely to encode the E1 component of PDH, was identified upstream from aceB. Transcriptional analysis revealed that aceA and aceB are expressed as a 5-kb polycistronic transcript from a promoter upstream of aceA. An intergenic region of 146 bp was located between aceA and aceB, and a 2-kb aceB transcript that originated from a promoter in the intergenic region was identified. DNA fragments upstream of aceA and aceB were shown to have promoter activities in P. aeruginosa, although only the aceA promoter was active in Escherichia coli. It is likely that the apparent pyoverdine-deficient phenotype of mutant OT2100 is a consequence of acidification of the growth medium due to accumulation of pyruvic acid in the absence of functional PDH.

Growth- and substrate-dependent transcription of the formate dehydrogenase (fdhCAB) operon in Methanobacterium thermoformicicum Z-245

The formate dehydrogenase-encoding fdhCAB operon and flanking genes have been cloned and sequenced from Methanobacterium thermoformicicum Z-245. fdh transcription was shown to be initiated 21 bp upstream from fdhC, although most fdh transcripts terminated or were processed between fdhC and fdhA. The resulting fdhC, fdhAB, and fdhCAB transcripts were present at all growth stages in cells growing on formate but were barely detectable during early exponential growth on H2 plus CO2. The levels of the fdh transcripts did, however, increase dramatically in cells growing on H2 plus CO2, coincident with the decrease in the growth rate and the onset of constant methanogenesis that occurred when culture densities reached an optical density at 600 nm of approximately 0.5. The mth transcript that encodes the H2-dependent methenyl-H4 MPT reductase (MTH) and the frh and mvh transcripts that encode the coenzyme F420-reducing (FRH) and nonreducing (MVH) hydrogenases, respectively, were also present in cells growing on formate, consistent with the synthesis of three hydrogenases, MTH, FRH, and MVH, in the absence of exogenously supplied H2. Reducing the H2 supply to M. thermoformicicum cells growing on H2 plus CO2 reduced the growth rate and CH4 production but increased frh and fdh transcription and also increased transcription of the mtd, mer, and mcr genes that encode enzymes that catalyze steps 4, 5, and 7, respectively, in the pathway of CO2 reduction to CH4. Reducing the H2 supply to a level insufficient for growth resulted in the disappearance of all methane gene transcripts except the mcr transcript, which increased. Regions flanking the fdhCAB operon in M. thermoformicicum Z-245 were used as probes to clone the homologous region from the Methanobacterium thermoautotrophicum deltaH genome. Sequencing revealed the presence of very similar genes except that the genome of M. thermoautotrophicum, a methanogen incapable of growth on formate, lacked the fdhCAB operon.

Isolation and characterization of a microspore-specific gene from tobacco

The characterization of a gene with a unique microspore-specific expression pattern is reported. Isolated microspores from tobacco were used to synthesize a cDNA library. Clones that did not hybridize to leaf cDNA were further characterized by northern analysis. One clone proved to be a microspore-specific cDNA, representing a transcript of 650 nt. The corresponding gene, NTM19 (Nicotiana tabacum microspore-specific), was isolated and its sequence analysed. The gene encodes a protein of 10.8 kDa with a pI of 6.92 and a putative signal sequence at the N-terminus. A localization study revealed a unique spatial and temporal distribution. The transcript was only detected in the unicellular microspore. No hybridization signals were observed in other pollen developmental stages, nor in the surrounding anther tissues or other vegetative tissues of the plant. Therefore it can be concluded that NTM19 is a gene with a highly microspore-specific character according to both localization and stage of expression. Southern blot analysis demonstrated the presence of a small gene family. The occurrence of TNM19 was investigated in a range of closely and distantly related species and was found to be present in other solanaceous species, including the ancestors of tobacco and in a monocot species.

Cloning, sequencing, and growth phase-dependent transcription of the coenzyme F420-dependent N5,N10-methylenetetrahydromethanopterin reductase-encoding genes from Methanobacterium thermoautotrophicum delta H and Methanopyrus kandleri

The mer genes, which encode the coenzyme F420-dependent N5,N10-methylenetetrahydromethanopterin reductases (CH2 = H4MPT reductases), and their flanking regions have been cloned from Methanobacterium thermoautotrophicum delta H and Methanopyrus kandleri and sequenced. The mer genes have DNA sequences that are 57% identical and encode polypeptides with amino acid sequences that are 57% identical and 71% similar, with calculated molecular masses of 33.6 and 37.5 kDa, respectively. In M. thermoautotrophicum, mer transcription has been shown to initiate 10 bp upstream from the ATG translation initiating codon and to generate a monocistronic transcript approximately 1 kb in length. This transcript was synthesized at all stages of M. thermoautotrophicum delta H growth in batch cultures but was found to increase in abundance from the earliest stages of exponential growth, reaching a maximum level at the mid-exponential growth phase. For comparison, transcription of the ftr gene from M. thermoautotrophicum delta H that encodes the formylmethanofuran:tetrahydromethanopterin formyltransferase (A. A. DiMarco, K. A. Sment, J. Konisky, and R. S. Wolfe, J. Biol. Chem. 265:472-476, 1990) was included in this study. The ftr transcript was found similarly to be monocistronic and to be approximately 1 kb in length, but, in contrast to the mer transcript, the ftr transcript was present at maximum levels at both the early and the mid-exponential growth stages.

3-D models of the antigenomic ribozyme of the hepatitis delta agent with eight new contacts suggested by sequence analysis of 188 cDNA clones

We mapped 359 mutations at 25 positions in synthetic variants of the antigenomic ribozyme of the hepatitis delta agent by analyzing the sequences of 188 cDNA clones. These data were used to identify three features of the ribozyme: highly conserved nucleotides, positions with restricted nucleotide substitutions and three-dimensional relationships between nucleotides. The distribution of mutations at the 25 positions was as follows: G-11 (the eleventh nucleotide from the cleavage site) was mutated in 56 clones; G-12 in 36; U-15 in 33; C-13 in 26; G-28 in 23; C-27 in 21; C-29 in 19; U-26 in 17; C-18 in 14; A-14 in 13; C-16 in 13; C-19 in 12; U-17 in 11; A-20 in 10; G-42 in 9; G-40 in 7; G-41 in 7; C-24 in 6; U-32 in 6; U-23 in 5; C-25 in 4; C-21 in 3; G-30 in 3; G-31 in 3; C-22 in 1. All clones containing a mutation at C-25 had an A at this position, suggesting that the extra cyclic amino group present in adenine and cytosine may function during the cleavage event. Mutations at certain positions were common in simple clones (containing only one or two mutations), while mutations at other positions were over-represented in more complex clones. Both compensatory base changes and co-mutational frequencies were used to identify eight pairs of nucleotides which may interact with each other: G-11 and C-18, G-12 and C-27, C-13 and G-28, C-21 and U-23/C-24, C-21 and G-30, U-23 and G-31/U-32, C24 and G-30, C-27 and G-42. These pairs, which involve some of the most conserved positions in the molecule, suggest interactions among nucleotides previously depicted in open-loop structures. The newly proposed points of contact between pairs of nucleotides are compatible with both the axehead and pseudoknot secondary structural models and were combined with previously proposed Watson-Crick base paired helices to produce two three dimensional models. In both of these, C-25 and C-76 are placed near the cleavage site.

Cloning and sequence analysis of the gene encoding the DNA polymerase I from Mycobacterium tuberculosis

The polA gene (encoding DNA polymerase I) from Mycobacterium tuberculosis was cloned using an internal gene segment probe generated by PCR amplification of genomic DNA [Mizrahi et al., Gene 136 (1993) 287-290]. The gene encodes a polypeptide 904 amino acids (aa) in length that shares 89% identity with a 911-aa homologue from Mycobacterium leprae. The polypeptide has all of the primary structural elements necessary for DNA polymerase and 5'-3' exonuclease activity, but lacks the motifs required for an associated 3'-5' exonuclease (proofreading) activity.

Mutational analysis of the herpes simplex virus virion host shutoff protein: evidence that vhs functions in the absence of other viral proteins

Herpes simplex virus (HSV) virions contain one or more factors that trigger rapid shutoff of host protein synthesis and accelerated decay of cellular and viral mRNAs in infected cells. HSV isolates bearing mutations at the virion host shutoff (vhs) locus (gene UL41) are defective for both processes, indicating that the vhs protein is required; however, it is not clear whether the role of vhs in shutoff is direct or indirect and if other virion components are also necessary. We therefore used a transient-cotransfection assay to determine if the vhs protein displays activity in the absence of other viral gene products. We found that a vhs expression vector strongly suppressed expression of a cotransfected lacZ reporter gene and that this effect was eliminated by the vhs1 point mutation that abolishes virion-induced host shutoff during HSV infection. Further evidence for the biological relevance of the transfection assay came from the demonstration that five vhs in-frame linker insertion mutations yielded concordant results when assayed in cotransfected cells and following transfer into the viral genome: three mutations eliminated activity in both assays, while two had no effect. On the basis of these results, we conclude that the vhs protein can trigger host shutoff in the absence of other HSV proteins. The cotransfection assay was used to rapidly assess the activities of a panel of linker insertion mutants spanning the vhs polypeptide. All mutations that mapped to regions conserved among the vhs homologs of alphaherpesvirus inactivated function; in contrast, four of five mutations that mapped to regions that are absent from several vhs homologs had no effect. These results further support the biological relevance of the transfection assay and begin to delineate functional domains of the vhs polypeptide.

Characterization of a 45-kDa flavoprotein and evidence for a rubredoxin, two proteins that could participate in electron transport from H2 to CO2 in methanogenesis in Methanobacterium thermoautotrophicum

Methanobacterium thermoautotrophicum strains contain a flavoprotein (flavoprotein A) that copurifies with the H2:heterodisulfide oxidoreductase complex. In this study, we report the iron-dependent synthesis and biochemical properties of flavoprotein A, cloning and sequencing of the flavoprotein-A-encoding gene (fpaA) and the co-transcription of fpaA with two downstream open reading frames, one of which (rdxA) appears to encode a rubredoxin. Native flavoprotein A has been shown to be a homodimer of a 45-kDa polypeptide that contains 1.3 mol FMN/45-kDa subunit but no iron or acid-labile sulfur. Catalytic amounts of the H2:heterodisulfide oxidoreductase complex or of the F420-reducing hydrogenase reduced flavoprotein A with H2, at specific rates of 0.3-0.4 U/mg enzyme, generating up to 70% flavin semiquinone before reduction to the flavin hydroquinone was observed. This intermediate accumulation of the semiquinone species had a kinetic rather than a thermodynamic basis, because the semiquinone form of flavoprotein A, generated by photoreduction, disproportionated quantitatively to the quinone and hydroquinone species. The midpoint potential of the quinone/hydroquinone couple was estimated to be 230 +/- 15 mV, at pH 7.6, versus the normal hydrogen electrode. Quantitation of Western blots demonstrated that flavoprotein A constituted approximately 1.5% of the soluble protein in cells grown in an iron-sufficient medium but that this increased to about 6% of the cellular protein when the iron the medium was depleted. The increase in the flavoprotein A content of cells grown under iron-limiting conditions was mirrored by a decrease in the content of the iron-rich polyferredoxin that also copurified with the H2:heterodisulfide oxidoreductase complex. The fpaA gene, cloned and sequenced from M. thermoautotrophicum strain delta H, encodes 404 amino acids in a sequence that has a C-terminal domain (approximately 130 amino acid residues) with features consistent with a flavodoxin structure. The remainder of flavoprotein A has sequences that are also predicted to be present in the N-terminal region of the orf14 gene product, which also appears to be an enlarged flavodoxin, encoded in the nif region of Rhodobacter capsulatus. Immediately downstream from fpaA, two open reading frames designated orfX and rdxA, have been located and shown by Northern-blot analyses to be co-transcribed with fpaA, although approximately 50% of fpaA-orfX-rdxA transcripts terminated or were cleaved within rdxA. Primer extension studies revealed that transcription of this transcriptional unit (the fpa operon) was initiated 32 nucleotides upstream of fpaA, at a site 25 nucleotides downstream from a sequence consistent with an archaeal TATA-box promoter element.(ABSTRACT TRUNCATED AT 400 WORDS)

Organization and growth phase-dependent transcription of methane genes in two regions of the Methanobacterium thermoautotrophicum genome

Two regions of the Methanobacterium thermoautotrophicum genome containing genes that encode enzymes involved in methanogenesis (methane genes) have been cloned and sequenced to determine the extent of methane gene clustering and conservation. One region from the M. thermoautotrophicum strains delta H and Winter, extending approximately 13.5 kb upstream from the adjacent mvhDGAB and mrtBDGA operons that encode the methyl-viologen-reducing hydrogenase (MVH) and the methyl coenzyme M reductase II (MRII), respectively, was sequenced, and 76% sequence identity and very similar gene organizations were demonstrated. Five closely linked open reading frames were located immediately upstream of the mvh operon and were designated flpECBDA. The flpCBD genes encode amino acid sequences that are 31, 47, and 65% identical to the primary sequences of the alpha and beta subunits of formate dehydrogenase and the delta subunit of MVH, respectively. Located immediately upstream of the flp genes was the mth gene, which encodes the H2-dependent methylene-tetrahydromethanopterin dehydrogenase (MTH). In contrast to this mth-flp-mvh-mrt cluster of methane genes, a separate approximately 5.4-kb genomic fragment cloned from M. thermoautotrophicum delta H contained only one methane gene, the mtd gene, which encodes the 8-hydroxy-5-deazaflavin (H2F420)-dependent methylene-tetrahydromethanopterin dehydrogenase (MTD). Northern (RNA) blot experiments demonstrated that mth was transcribed only at early growth stages in fermentor-grown cultures of M. thermoautotrophicum delta H, whereas mtd was transcribed at later growth stages and in the stationary phase. Very similar transcription patterns have been observed by T.D. Pihl, S. Sharma, and J. N. Reeve (J. Bacteriol. 176:6384-6391, 1994) for the MRI- and MRII-encoding operons, mrtBDGA and mcrBDCGA, im M. thermoautotrophicum deltaH, suggesting coordinated regulation of methane gene expression. In contrast to the growth phase-dependent transcription of the mth/mrt and mtd/mcr genes, transcription of the mvhDGAB and frhADGB operons, which encode the two (NiFe) hydrogenases in M. thermoautotrophicum deltaH, was found to occur at all growth stages.

Isolation and sequence analysis of cDNAs encoding phosphoenolpyruvate carboxykinase from the PCK-type C4 grass Urochloa panicoides

A rabbit antiserum was raised against phosphoenolpyruvate carboxykinase (PCK) purified from Urochloa panicoides, a PCK-type C4 monocot. The antiserum was used to screen a cDNA expression library constructed from U. panicoides leaf poly(A)+RNA. Inserts from immunoreactive clones were used to rescreen the library and obtain three overlapping cDNAs comprising a 2220 bp composite sequence. The single complete open reading frame of 1872 bp encodes PCK1, a 624 amino acid polypeptide with a predicted molecular mass of 68,474 Da. Comparison of PCK1 with other ATP-dependent PCKs indicates that PCK1 is significantly larger, mainly due to an N-terminal extension of greater than 65 residues, and reveals high sequence identity across the central portion of the protein, especially over seven sub-sequences. One of these sub-sequences spans motifs common to several ATP-utilising enzymes for phosphate and divalent cation binding. The anti-PCK antiserum recognises a 69 kDa polypeptide on immunoblots of either purified PCK or U. panicoides leaf extracts. However, polypeptides of 63, 62, 61 and 60 kDa are also immunoreactive. Amino terminal sequencing of polypeptides from preparations of purified PCK demonstrates that these smaller polypeptides are related to PCK1, and time course experiments show that these polypeptides arise from the breakdown of PCK during isolation. Northern blot analysis indicates that the 2.7 kb PCK mRNA is abundant in green leaves but not in roots or etiolated shoots. Moreover, PCK mRNA levels increase gradually during greening, reaching maximum levels after about 84 h.

Sequence analysis of the nucleoprotein genes of three enterotropic strains of murine coronavirus

The nucleotide sequences of the nucleoprotein genes of three enterotropic strains of the murine coronavirus mouse hepatitis virus (MHV-Y, MHV-RI and DVIM) were determined and compared with previously reported sequences of three polytropic (respiratory) strains (MHV-A59, MHV-JHM and MHV-S). Greater than 92% homology was found among the six strains by pair-wise comparison at the nucleotide level. The genes encoded proteins of 451 to 455 residues and the deduced amino acid sequences were more than 91% homologous. A unique deletion of twelve nucleotides was found at the carboxy terminus of MHV-Y and a three nucleotide deletion was found in MHV-RI, which corresponded to the one previously reported in MHV-A59 and MHV-S. Two internal open reading frames were found within the coding region of the nucleoprotein, the smaller one was specific for the enterotropic strains. It could potentially encode a truncated version of the hypothetical protein described for MHV-A59 and MHV-S. Sequence relationship of the N gene showed no correlation with tissue tropism and no sequence or even single amino acid change unique to either tropism group was found. This indicates that the nucleoprotein of MHV probably has no part in the determination of the primary tissue tropism of an MHV strain. The role of the potential internal protein warrants further investigation.