High GC Research Articles

DNA tandem repeats contribute to the genetic diversity of Brevibacterium aurantiacum phages.

This report presents the characterization of the first virulent phages infecting Brevibacterium aurantiacum, a bacterial species used during the manufacture of surface-ripened cheeses. These phages were also responsible for flavour and colour defects in surface-ripened cheeses. Sixteen phages (out of 62 isolates) were selected for genome sequencing and comparative analyses. These cos-type phages with a long non-contractile tail currently belong to the Siphoviridae family (Caudovirales order). Their genome sizes vary from 35,637 to 36,825 bp and, similar to their host, have a high GC content (~61%). Genes encoding for an immunity repressor, an excisionase and a truncated integrase were found, suggesting that these virulent phages may be derived from a prophage. Their genomic organization is highly conserved, with most of the diversity coming from the presence of long (198 bp) DNA tandem repeats (TRs) within an open reading frame coding for a protein of unknown function. We categorized these phages into seven genomic groups according to their number of TR, which ranged from two to eight. Moreover, we showed that TRs are widespread in phage genomes, found in more than 85% of the genomes available in public databases.

Efficient Multiplex Genome Editing in Streptomyces via Engineered CRISPR-Cas12a Systems.

Streptomyces strains produce a great number of valuable natural products. With the development of genome sequencing, a vast number of biosynthetic gene clusters with high potential for use in the discovery of valuable clinical drugs have been revealed. Therefore, emerging needs for tools to manipulate these biosynthetic pathways are presented. Although the clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas 9) system has exhibited great capabilities for gene editing in multiple Streptomyces strains, it has failed to work in some newly discovered strains and some important industrial strains. Additionally, the protospacer adjacent motif (PAM) recognition scope of this system sometimes limits its applications for generating precise site mutations and insertions. Here, we developed three efficient CRISPR-FnCas12a systems for multiplex genome editing in several Streptomyces strains. Each system exhibited advantages for different applications. The CRISPR-FnCas12a1 system was efficiently applied in the industrial strain Streptomyces hygroscopicus, in which SpCas9 does not work well. The CRISPR-FnCas12a2 system was used to delete large fragments ranging from 21.4 to 128 kb. Additionally, the CRISPR-FnCas12a3 system employing the engineered FnCas12a mutant EP16, which recognizes a broad spectrum of PAM sequences, was used to precisely perform site mutations and insertions. The CRISPR-FnCas12a3 system addressed the limitation of TTN PAM recognition in Streptomyces strains with high GC contents. In summary, all the CRISPR-FnCas12a systems developed in this study are powerful tools for precise and multiplex genome editing in Streptomyces strains.

Nascent Transcript Folding Plays a Major Role in Determining RNA Polymerase Elongation Rates

SummaryTranscription elongation rates influence RNA processing, but sequence-specific regulation is poorly understood. We addressed this in vivo, analyzing RNAPI in S. cerevisiae. Mapping RNAPI by Miller chromatin spreads or UV crosslinking revealed 5′ enrichment and strikingly uneven local polymerase occupancy along the rDNA, indicating substantial variation in transcription speed. Two features of the nascent transcript correlated with RNAPI distribution: folding energy and GC content in the transcription bubble. In vitro experiments confirmed that strong RNA structures close to the polymerase promote forward translocation and limit backtracking, whereas high GC in the transcription bubble slows elongation. A mathematical model for RNAPI elongation confirmed the importance of nascent RNA folding in transcription. RNAPI from S. pombe was similarly sensitive to transcript folding, as were S. cerevisiae RNAPII and RNAPIII. For RNAPII, unstructured RNA, which favors slowed elongation, was associated with faster cotranscriptional splicing and proximal splice site use, indicating regulatory significance for transcript folding.

Hydrophobic Amino Acids as Universal Elements of Protein-Induced DNA Structure Deformation

Interaction with the DNA minor groove is a significant contributor to specific sequence recognition in selected families of DNA-binding proteins. Based on a statistical analysis of 3D structures of protein–DNA complexes, we propose that distortion of the DNA minor groove resulting from interactions with hydrophobic amino acid residues is a universal element of protein–DNA recognition. We provide evidence to support this by associating each DNA minor groove-binding amino acid residue with the local dimensions of the DNA double helix using a novel algorithm. The widened DNA minor grooves are associated with high GC content. However, some AT-rich sequences contacted by hydrophobic amino acids (e.g., phenylalanine) display extreme values of minor groove width as well. For a number of hydrophobic amino acids, distinct secondary structure preferences could be identified for residues interacting with the widened DNA minor groove. These results hold even after discarding the most populous families of minor groove-binding proteins.

Complete Genome of Lactobacillus iners KY Using Flongle Provides Insight Into the Genetic Background of Optimal Adaption to Vaginal Econiche.

Despite the importance of Lactobacillus iners and its unique characteristics for the study of vaginal adaption, its genome and genomic researches for identifying molecular backgrounds of these specific phenotypes are still limited. In this study, the first complete genome of L. iners was constructed using a cost-effective long-read sequencing platform, Flongle from Oxford Nanopore, and comparative genome analysis was conducted using a total of 1,046 strain genomes from 10 vaginal Lactobacillus species. Single-molecule sequencing using Flongle effectively resolved the limitation of the 2nd generation sequencing technologies in dealing with genomic regions of high GC contents, and comparative genome analysis identified three potential core genes (INY, ZnuA, and hsdR) of L. iners which was related to its specific adaption to the vaginal environment. In addition, we performed comparative prophage analysis for 1,046 strain genomes to further identify the species specificity. The number of prophages in L. iners genomes was significantly smaller than other vaginal Lactobacillus species, and one of the specific genes (hsdR) was suggested as the means for defense against bacteriophage. The first complete genome of L. iners and the three specific genes identified in this study will provide useful resources to further expand our knowledge of L. iners and its specific adaption to the vaginal econiche.

Molecular determinants of outcome for metastatic castration-sensitive prostate cancer (mCSPC) with addition of apalutamide (APA) or placebo (PBO) to androgen deprivation therapy (ADT) in TITAN.

5535 Background: In TITAN, addition of APA to ADT improved radiographic progression-free survival (rPFS) and overall survival (OS) versus PBO plus ADT in patients (pts) with mCSPC. In this post hoc analysis, we performed transcriptome-wide profiling of tumor samples and assessed association of molecular subtypes with rPFS. Methods: The DECIPHER platform (Decipher Biosciences, Inc.) was used to assess gene expression in archival primary prostate tumors from TITAN. Samples were classified into high versus low to average risk of metastases (DECIPHER genomic classifier [GC] > 0.6 and ≤ 0.6, respectively), basal and luminal A/B (PAM50 classifier), and androgen receptor activity (AR-A) signature high and low. Associations between subtypes with rPFS were assessed with Cox proportional hazards model. Results: The biomarker population included 222 pts (APA, 110; PBO, 112). Benefit in rPFS from APA in the biomarker population (HR [95% CI]; p value; 0.49 [0.31-0.78]; 0.002) resembled that in the overall study population (0.49 [0.40-0.61]; < 0.0001). The majority of TITAN pts had GC high scores (n = 166, 75%). GC high risk subtype in the PBO group had poorer prognosis for rPFS than GC low to average risk subtype (median rPFS 18.2 mos for GC high vs not reached [NR] for GC low to average, 0.28 [0.11-0.69]; 0.006), but there was no difference in prognosis between high and low to average GC risk subtypes in the APA group (GC high NR vs GC low to average NR; 0.81 [0.35-1.89]; 0.625). Pts were further stratified based on basal/luminal and AR-A signatures. Basal (n = 112, 50%) and AR-A low (n = 96, 43%) subtypes, known to be nonresponsive to ADT, both showed significant benefit from APA vs PBO (0.30 [0.16-0.57]; < 0.001 and 0.25 [0.12-0.52]; < 0.001, respectively). The majority of AR-A low subtype (74%, 71/96) overlapped with basal subtype. Further conclusions for risk of rPFS in GC low, luminal, and AR-A high subtypes and OS across all subtypes will be assessed as more events occur. Conclusions: In TITAN, addition of APA to ADT improved rPFS for all subtypes of pts with mCSPC. APA overcame the poor prognosis of GC high risk subtype and prolonged rPFS in ADT-resistant AR-A low and basal molecular subtypes, suggesting APA is beneficial especially for the highest risk molecular subtypes. Clinical trial information: NCT02489318 .

The development and validation of a novel targeted methylation sequencing technology detecting 0.003 percent tumor signal in early-stage cancer plasma.

4092 Background: Methylation analysis in cell-free DNA holds great potential for early cancer detection. In the plasma of early stage cancer patient, the tumor content is estimated to be less than 0.1%, therefore demands a highly sensitive assay. Targeted Methylation Sequencing (TMS) is the most promising approach; however, the current sensitivity and specificity are compromised by low efficiency and low recovery of target enrichment, and further hampered by background noise associated with large panels. The ideal solution would be an in-depth analysis using a focused small cancer-specific methylation biomarker panel, but is not supported by existing technologies. Methods: Here we present a new technology designed for TMS analysis in cfDNA: Point-n-Seq, featuring an enrichment of target molecules directly from cfDNA before bisulfite conversion and amplification. Particularly, this technology enables small focused panel that interrogates the methylation status of 1 to ~1000 markers. We designed a CRC panel covering 100 methylation markers in 3 steps: identify ~1000 CRC-specific markers from public databases; eliminate makers with high background signal in baseline cfDNA of healthy population; finalize the list with the most differentiating markers between patient and healthy cfDNA. Results: The capture of Point-n-Seq CRC panel is highly efficient resulting in high uniformity (94% > 0.5X) and on-target rate ( > 80%). For 20 ng cfDNA input, more than 1000 deduped informative reads were obtained for each marker on average, despite the high GC content ( > 80%). The output of informative reads was linear to the cfDNA input ranging from 1 ng to 40 ng. In titration studies, 0.6 pg (0.2X genome equivalent) methylated DNA in 20 ng cfDNA (0.003%) was reliably detected over cfDNA background. Using plasma samples from patients with CRC - early stage (I, n = 7; II, n = 7), late stage (III, n = 11; IV, n = 3), and control individuals (n = 105), the average fractions of methylated signal are 0.0034%, 0.013%, 0.09%, 0.17%, 0.29% for control, stage I, II, III, IV accordingly. With a simple cut-off using methylation fraction, Point-n Seq CRC panel achieved a sensitivity of 86% for stage I, 100% for stage (II-IV) at a specificity of 91%, with AUC = 0.96. Conclusions: Point-n-Seq TMS is the first hybridization based NGS technology enables the small focused methylation panel (e.g. 100 markers) sequencing using cfDNA, and it will greatly facilitate the development of practical and cost-effective methylation assays for clinical use.

Complete Genome Sequence of Janibacter melonis M714, a Janus-Faced Bacterium with Both Human Health Impact and Industrial Applications.

Janibacter, a member of the Intrasporangiaceae family of Actinobacteria, is a Janus-faced bacterium that has both antibiotic resistance/pathogenicity and the ability to degrade pollutants, with significant research value. Here, we isolated the novel strain Janibacter melonis M714 from an irradiated area in Xinjiang Uygur Autonomous Region, China. J. melonis M714 contains one circular chromosome of 3,426,637 bp with a GC content of 72.98% and one plasmid of 54,436bp with a GC content of 67.80%. The genome of J. melonis M714 contains 2,859 CDSs, 47 tRNA genes, and 6 rRNA genes. Genome assembly and annotation indicated that strain M714 has a high GC content and contains multiple notable functional genes, including a beta-lactam resistance gene and dioxygenase gene, which may be the key determinants of the strain's antibiotic resistance and xenobiotic degradation ability, respectively. The whole genome sequences of J. melonis M714 provide information that is useful for its potential applications in the degradation of pollutants and environmental remediation.

Molecular Characterization of Two Catfish Species (Chrysichthys nigrodigitatus and Chrysichthys auratus) from the Cross River, Nigeria, Using Ribosomal RNA and Internal Transcribed Spacers

Studies were conducted on Chrysichthys nigrodigitatus and C. auratus from the Cross River, Nigeria. The objective was to document intra- and inter-specific variations in molecular structure among four populations of the genus in the river. DNA was extracted from caudal fin and primers designed for the ribosomal RNA and Internal Transcribed Spacer Region were used for amplification. Molecular characterization yielded a fragment containing partial sequences of 18S rRNA, ITS-1, ITS-2 and 28S rRNA genes and a complete sequence of 5.8S rRNA. The 5.8S rRNA was the only gene amplified consistently in all samples indicating that it is more conserved among the samples studied. The percentage of GC contents fall within the range observed in other catfish species. They were generally higher in C. auratus than in C. nigrodigitatus and also higher than the AT contents in both species. The high GC content could be an adaptation to warmer climates. Alignment of the nucleotide sequences of the two species from the two regions showed that the rRNA and ITS genes are highly conserved with >99% nucleotide identity. However, a total of 284 single nucleotide polymorphisms (SNPs) were observed in these genes in the two species, made up of deletions (0.35%), single base insertions (11.27%), multiple base insertions (14.39%), single base transition substitutions (29.93%), single base transversion substitutions (33.8%) and multiple base substitutions (11.27%). The overall ratio of transition to transversion polymorphisms was approximately 1: 1 indicating a low level of genetic instability in Chrysichthys spp. The indels were responsible for length variations in the sequences. Sequence information for the ITS region of these fishes is reported for the first time. This study has provided an insight into polymorphism patterns of these genes in Chrysichthys spp across the four populations studied which could form the basis for further genomic characterization and mapping of these species.

Biochemical analysis of PriA Helicases from Gram‐positive Bacteria involved in DNA Replication Restart

DNA replication forks often encounter template DNA lesions, which can stall progression of the replication forks. In gram‐positive bacteria, the PriA‐dependent pathway is the major replication restart mechanism and it requires several primosome proteins. Among them, the PriA protein—a 3′ to 5′ superfamily‐2 DNA helicase—is the key factor recognizing DNA lesions and it further recruits other proteins. Here, we investigated the PriA ATPase and helicase activities of Streptococcus pneumoniae (SpPriA) and Geobacillus stearothermophilus (GstPriA) through biochemical and kinetic analyses. Using various DNA duplexes with unstructured single‐stranded regions, we observed distinct unwinding abilities for GstPriA and SpPriA according to increased GC content of duplex DNA substrate. In contrast to the unwinding activity of GstPriA helicase, we found that SpPriA is unable to unwind duplex DNA substrate with high GC content. However, the presence of DnaD loader protein allows SpPriA to unwind such duplex DNA. Our findings suggest that SpPriA possesses limited unwinding ability in high GC DNA and that DnaD acts as an accessory protein to destabilize stalled replication forks through its single‐stranded DNA binding ability, thereby enhancing PriA unwinding activity.

Association of Melanophilin (MLPH) gene polymorphism with coat colour in Rex rabbits

Rex rabbit, with multiple phenotypes and colourful fur, is an interesting model for assessing the effect of coat colour gene mutations on characteristic pigmentation phenotype. Based on previous study, the <em>melanophilin</em> (<em>MLPH</em>) gene is a positional candidate gene related coat colour dilution. The fur colours are a lighter shade, e.g. grey instead of black. We sequenced 1689 base pairs of the <em>MLPH</em> gene in Chinchilla and black Rex rabbit. A total of 13 polymorphisms were identified, including seven missense mutations. The rabbit <em>MLPH</em> gene has a very high GC content and the protein shows 64.87% identity to the orthologous human protein (lack of homologous amino acids encoded by human MLPH exon 9). Hardy-Weinberg test showed that, except for the g.606C>A single nucleotid polymorphism (SNP), all other SNPs were in Hardy-Weinberg equilibrium. Haplotype analysis revealed that the seven missense mutation SNPs of two strains of Rex rabbits formed 10 haplotypes, but there were only seven major types of haplotypes (haplotype frequency <em>P</em>>0.05). The major haplotypes of the Chinchilla and black Rex rabbits were H1/H2/H3/H4/H5 and H1/H2/H3/H6/H8, respectively. The special haplotypes of Chinchilla Rex rabbit (H4, H5, H7) were consistently associated with the Chinchilla phenotype. This study provides evidence that different coat colour formation may be caused by one or more mutations within <em>MLPH</em> gene in several Rex rabbit strains. The data on polymorphisms that are associated with the Chinchilla phenotype facilitate the breeding of rabbits with defined coat colours.

Cloning, expression and purification of the low-complexity region of RanBP9 protein

Recombinant expression and purification of proteins is key for biochemical and biophysical investigations. Although this has become a routine and standard procedure for many proteins, intrinsically disordered ones and those with low complexity sequences pose difficulties. Proteins containing low complexity regions (LCRs) are increasingly becoming significant for their roles in both normal and pathological processes. Here, we report cloning, expression and purification of N-terminal LCR of RanBP9 protein (Nt-RanBP9). RanBP9 is a scaffolding protein present in both cytoplasm and nucleus that is implicated in many cellular processes. Nt-RanBP9 is a poorly understood region of the protein perhaps due to difficulties posed by the LCR. Indeed, conventional methods presented difficulties in Nt-RanBP9 cloning due to its high GC content resulting in insignificant protein expression. These led us to use a different approach of cloning by expressing the protein as a fusion construct containing mCherry or mEGFP using in vivo DNA recombination methods. Our results indicate that expression of mEGFP-tagged Nt-RanBP9 followed by thrombin cleavage of the tag was the most effective method to obtain the protein with >90% purity and good yields. We report and discuss the challenges in obtaining the N-terminal region of RanBP9, a protein with functional implications in multiple biological processes and neurodegenerative diseases.

Plastome-based phylogenomics resolves the placement of the sanguinolenta group in the spikemoss of lycophyte (Selaginellaceae)

Selaginellaceae have been shown to be monophyletic in previous studies, and include only the single genus Selaginella. However, the two most recent classifications of the genus disagree in terms of the number of subgenera recognized, and the position of problematic clades such as the “sanguinolenta” group, which has been resolved in quite different positions in different studies. Here, we performed a plastid-genome based phylogenomic analysis of Selaginellaceae to address this problem. The sanguinolenta group, represented here by three species, was resolved as sister to the remaining members of subg. Stachygynandrum. Additionally, subg. Exaltatae, subg. Ericetorum, and subg. Gymnogynum in clade A clustered into a well supported monophyletic clade but with conflicting topology between subgenera inside, which is possibly attributed to the early divergence among them. We uncovered substantial variation in both synonymous (dS) and nonsynonymous (dN) substitution rate, and GC content in plastomes of Selaginellaceae. The values of dS, dN, and GC content were significantly higher than those of other lycophytes (Isoetaceae and Lycopodiaceae). We observed a significant positive correlation between the high GC content, and the elevated dS and dN rates. In addition, the dS and dN values inferred among branches of Selaginellaceae were extremely variable. Our data indicate that this unevenly distributed substitution rate likely reflected relaxed or intensified selection among different lineages, which is possibly related to the inconsistency of the subgeneric phylogenetic topologies of Selaginellaceae.

Human Telomerase Reverse Transcriptase Gene Promoter Mutation in Serum of Patients with Hepatocellular Carcinoma

Background: Mutations in the human telomerase reverse transcriptase (hTERT) gene promoter have been reported in hepatocellular carcinoma (HCC); however, analyses of these mutations in liquid biopsies have been technically difficult because of the high GC content of the regions of interest within this promoter. We evaluated the feasibility and prognostic value of hTERT promoter mutations identified in circulating cell-free DNA (cfDNA) from the serum of patients with HCC. Objective: A cohort of HCC patients (n = 36) who were curatively treated by surgical resection between June 2003 and September 2014 were enrolled in this study. Methods: The presence of hTERT promoter mutations in cfDNA from the patients’ serum was analyzed via modified droplet digital polymerase chain reaction, and associations were sought between specific promoter mutations and patients’ disease-free survival (DFS). Results: The G>A hTERT mutation at –124 bp was detected in the serum of 25 patients (69%). Although no marked differences were observed between the characteristics of the serum mutation-positive and serum mutation-negative patient groups, the DFS of patients with the mutation was significantly shorter than that of the serum mutation-negative patients (p = 0.02). Among 18 clinicopathologic and background liver factors examined, the presence of the –124 bp G>A mutation was an independent and significant predictor of patients’ DFS (hazard ratio = 3.01, 95% confidence interval 1.11–10.5, p = 0.03) in multivariate analyses. Conclusions: The –124 bp G>A hTERT promoter mutation was observed in the serum of 69% of HCC patients who underwent surgical resection and was an independent predictor of disease progression in HCC.

Unusual sequence characteristics of human chromosome 19 are conserved across 11 nonhuman primates

BackgroundHuman chromosome 19 has many unique characteristics including gene density more than double the genome-wide average and 20 large tandemly clustered gene families. It also has the highest GC content of any chromosome, especially outside gene clusters. The high GC content and concomitant high content of hypermutable CpG sites raises the possibility chromosome 19 exhibits higher levels of nucleotide diversity both within and between species, and may possess greater variation in DNA methylation that regulates gene expression.ResultsWe examined GC and CpG content of chromosome 19 orthologs across representatives of the primate order. In all 12 primate species with suitable genome assemblies, chromosome 19 orthologs have the highest GC content of any chromosome. CpG dinucleotides and CpG islands are also more prevalent in chromosome 19 orthologs than other chromosomes. GC and CpG content are generally higher outside the gene clusters. Intra-species variation based on SNPs in human common dbSNP, rhesus, crab eating macaque, baboon and marmoset datasets is most prevalent on chromosome 19 and its orthologs. Inter-species comparisons based on phyloP conservation show accelerated nucleotide evolution for chromosome 19 promoter flanking and enhancer regions. These same regulatory regions show the highest CpG density of any chromosome suggesting they possess considerable methylome regulatory potential.ConclusionsThe pattern of high GC and CpG content in chromosome 19 orthologs, particularly outside gene clusters, is present from human to mouse lemur representing 74 million years of primate evolution. Much CpG variation exists both within and between primate species with a portion of this variation occurring in regulatory regions.

Rare species in the structure of acid-resistent members of the order Actinomycetales isolated from clinical material.

The article presents data on the structure of acid-resistant members of the order Actinomycetales and rare species that have been isolated and identified using various methods. The study included strains of non-tuberculous mycobacteria (NTM) isolated from clinical material during examination for tuberculosis in the period from 2016 to 2019. The total number of samples with signs of NTMs growth that were included in the study was 316 samples. Primary isolation on Levenshtein-Jensen, Finn II, and MGIT media and NTMs identification by DNA-hybridization. All strains that were not identified prior to the species and culture, identified as microorganisms with a high G+C content (High GC GR +) were re-identified using a MALDI-ToF Microflex LT mass spectrometer (Bruker®). By the method of DNA-hybridization, 188 strains isolated by NTM were successfully identified to form 58.5% of all selected cultures. Among the selected species, representatives of slowly growing NTMs (M. avium complex, M. gordonae, M. kansasii) predominated, which amounted to 67.0% of all NTM strains identified to the species. Among the cultures for which DNA hybridization failed to carry out acceptable identification, predominantly NTMs were found, among which M. gordonae, M. avium, M. kansasii dominated. A number of NTMs were represented by rare species: M. iranicum and M. pseudoshottsii. Among this group of microorganisms, other acid-resistant aerobic actinomycetes were isolated, including those of potential clinical significance: Gordonia spp., Tsukamurella spp., Rhodococcus spp., Nocardia spp. When identifying cultures containing high concentrations of G+C, the maximum number of microbial associations was revealed, including those consisting of two types of NTMs (M. monacense + M. flavescens, M. avium + M. kansasii), as well as associations of M. gordonae with staphylococci. The same group included rare NTM species: M. fredericbergense, M. szulgai, M. malmoense, M. bohemicum, M. septicum, as well as representatives of the genera Nocardia, Gordonia, Tsukamurella.

Bending and looping of long DNA by Polycomb repressive complex 2 revealed by AFM imaging in liquid.

Polycomb repressive complex 2 (PRC2) is a histone methyltransferase that methylates histone H3 at Lysine 27. PRC2 is critical for epigenetic gene silencing, cellular differentiation and the formation of facultative heterochromatin. It can also promote or inhibit oncogenesis. Despite this importance, the molecular mechanisms by which PRC2 compacts chromatin are relatively understudied. Here, we visualized the binding of PRC2 to naked DNA in liquid at the single-molecule level using atomic force microscopy. Analysis of the resulting images showed PRC2, consisting of five subunits (EZH2, EED, SUZ12, AEBP2and RBBP4), bound to a 2.5-kb DNA with an apparent dissociation constant ($K_{\rm{D}}^{{\rm{app}}}$) of 150 ± 12 nM. PRC2 did not show sequence-specific binding to a region of high GC content (76%) derived from a CpG island embedded in such a long DNA substrate. At higher concentrations, PRC2 compacted DNA by forming DNA loops typically anchored by two or more PRC2 molecules. Additionally, PRC2 binding led to a 3-fold increase in the local bending of DNA's helical backbone without evidence of DNA wrapping around the protein. We suggest that the bending and looping of DNA by PRC2, independent of PRC2's methylation activity, may contribute to heterochromatin formation and therefore epigenetic gene silencing.

Study on the Effective Method of Optimizing PCR-DGGE by adding PCR enhancers

PCR-based denaturing gradient gel electronic (PCR-DGGE) has become a frequently used method in the determination of bacteria community in water, soil and other habitats. However, the precision and the integrality of microbiology community by this approach should be reinforced and the key for this is optimization on PCR for which is the basis of PCR-DGGE. Aiming at this, PCR enhancer combinations were applied in both two amplification rounds of PCR-DGGE in this study. The results showed that many new bands were produced and originally weak bands were intensified after the addition of PCR enhancer combinations, particularly DBD-2 (1% DMSO, 0.4 M Betaine, 1mM DTT) in PCR amplification buffer system. Virtually all newly appeared bands in DGGE were probably derived from the bacteria with high GC% content (60%). Thus the major optimization on PCR-DGGE was PCR enhancer may contribute to decreasing annealing temperature and improving the PCR product yields of the high-GC%-contented bacteria. In conclusion, PCR enhancers could remarkably improve the amplification efficacy, particularly for using the complex and tiny environmental DNA or weaker bands from DGGE as PCR template, and furthermore increase the detected bacterial species in PCR-DGGE. Therefore we strongly proposed that the PCR enhancer combination be routinely applied in PCR-DGGE for the bacterial community determination.

High GC Content DNA does not Affect Phage T4 DNA Packaging -- Test of a Scrunchworm Model for Packaging Motor Function

Many viruses use an ATP-powered DNA translocating molecular motor during assembly to package their genomes into preformed viral capsid shells. These powerful motors can generate >60 pN of force and translocate DNA at up to ∼2000 bp/s. One model for motor function, the “scrunchworm model”, proposed that the segment of DNA threaded through the motor-portal channel could be repeatedly induced to transition between longer and shorter structural forms. One version of the model hypothesized that transitions between the B- and A-form DNA might drive translocation and predicted that high GC content would alter motor function. We conducted single-molecule measurements of phage T4 packaging with optical tweezers and do not find any evidence that motor function is altered. Our results suggest that if the motor operates by a scrunchworm-type mechanism the DNA transitions are different than B-to-A form transitions.

Complete genome sequence of Bifidobacterium adolescentis P2P3, a human gut bacterium possessing strong resistant starch-degrading activity.

Resistant starch (RS) is an important food source from which gut bacteria produce short chain fatty acids, which have beneficial effects for human health. The Bifidobacterium adolescentis P2P3, a human gut bacterium possessing a strong RS-degrading activity, was isolated from a healthy Korean adult male. In vitro experiments showed that this bacterium could utilize approximately 63% of high amylose corn starch after forming RS granule clusters. Here we provide the first complete set of genomic information on RS-degrading B. adolescentis P2P3. The genome of B. adolescentis P2P3 consists of one chromosome (2,202,982bp) with high GC content (59.4%). Analysis of the protein-coding genes revealed that at least nineteen of the starch degradation-related enzymes were present in the genome. Among those, five genes evidently possess carbohydrate-binding domains, which are presumed to be involved in efficient RS decomposition. The complete set of genomic information on B. adolescentis P2P3 could provide an understanding of the role of RS-degrading gut bacteria and its RS degradation mechanism.