Dbf4 recruitment by forkhead transcription factors defines an upstream rate-limiting step in determining origin firing timing.

Initiation of eukaryotic chromosome replication follows a spatiotemporal program. The current model suggests that replication origins compete for a limited pool of initiation factors. However, it remains to be answered how these limiting factors are preferentially recruited to early origins. Here, we report that Dbf4 is enriched at early origins through its interaction with forkhead transcription factors Fkh1 and Fkh2. This interaction is mediated by the Dbf4 C terminus and was successfully reconstituted in vitro. An interaction-defective mutant, dbf4ΔC, phenocopies fkh alleles in terms of origin firing. Remarkably, genome-wide replication profiles reveal that the direct fusion of the DNA-binding domain (DBD) of Fkh1 to Dbf4 restores the Fkh-dependent origin firing but interferes specifically with the pericentromeric origin activation. Furthermore, Dbf4 interacts directly with Sld3 and promotes the recruitment of downstream limiting factors. These data suggest that Fkh1 targets Dbf4 to a subset of noncentromeric origins to promote early replication in a manner that is reminiscent of the recruitment of Dbf4 to pericentromeric origins by Ctf19.

Optimization of the Preparation Process of Glucuronomannan Oligosaccharides and Their Effects on the Gut Microbiota in MPTP-Induced PD Model Mice.

Parkinson's disease (PD) is a prevalent neurodegenerative disorder, and accumulating evidence suggests a link between dysbiosis of the gut microbiota and the onset and progression of PD. In our previous investigations, we discovered that intraperitoneal administration of glucuronomannan oligosaccharides (GMn) derived from Saccharina japonica exhibited neuroprotective effects in a 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced PD mouse model. However, the complicated preparation process, difficulties in isolation, and remarkably low yield have constrained further exploration of GMn. In this study, we optimized the degradation conditions in the preparation process of GMn through orthogonal experiments. Subsequently, an MPTP-induced PD model was established, followed by oral administration of GMn. Through a stepwise optimization, we successfully increased the yield of GMn, separated from crude fucoidan, from 1~2/10,000 to 4~8/1000 and indicated the effects on the amelioration of MPTP-induced motor deficits, preservation of dopamine neurons, and elevation in striatal neurotransmitter levels. Importantly, GMn mitigated gut microbiota dysbiosis induced by MPTP in mice. In particular, GM2 significantly reduced the levels of Akkermansia, Verrucomicrobiota, and Lactobacillus, while promoting the abundance of Roseburia and Prevotella compared to the model group. These findings suggest that GM2 can potentially suppress PD by modulating the gut microbiota, providing a foundation for the development of a novel and effective anti-PD marine drug.

Identification and genome-wide analysis provide insights into the genetic diversity and biotechnological potentials of novel cold-adapted Acinetobacter strain.

Extreme cold environments, such as polar regions or high-altitude mountains, are known for their challenging conditions including low temperatures, high salinity, and limited nutrient availability. Microbes that thrive in these environments have evolved specialized strategies to survive and function under such harsh conditions. The study aims to identify, sequence the genome, perform genome assembly, and conduct a comparative genome-wide analysis of Acinetobacter sp. strain P1, which was isolated from the Batura glacier regions of Pakistan. A basic local alignment search tool of NCBI using 16 s RNA gene sequence confirmed the strain Acinetobacter following phylogenetic analysis revealed that strain P1 clustered with Acinetobacter sp. strain AcBz01. The high-throughput Genome sequencing was done by the NovaSeq 6000 sequencing system following de novo genome assembly reported 23 contigs, a genome size of 3,732,502 bp containing approximately 3489 genes and 63 RNAs (60 tRNA, 3 rRNA). The comparative genome analysis revealed that Acinetobacter sp. strain P1 exhibited the highest homology with the Acinetobacter baumannii ATCC 17978 genome and encompassed 1668 indispensable genes, 1280 conserved genes 1821 specific genes suggesting high genomic plasticity and evolutionary diversity. The genes with functional assignments include exopolysaccharide phosphotransferase enzyme, cold-shock proteins, T6SS, membrane modifications, antibiotic resistance, and set of genes related to a wide range of metabolic characteristics such as exopolysaccharides were also present. Moreover, the structural prediction analysis of EPS proteins reveals that structural flexibility allows for conformational modifications during catalysis, which boosts or increases the catalytic effectiveness at lower temperatures. Overall, the identification of Acinetobacter, a cold-adapted bacterium, offers promising applications in bioremediation, enzyme production, food preservation, pharmaceutical development, and astrobiology. Further research and exploration of these microorganisms can unlock their full biotechnological potential and contribute to various industries and scientific endeavors.

A genome-wide genetic linkage map and reference quality genome sequence for a new race in the wheat pathogen Pyrenophora tritici-repentis.

Pyrenophora tritici-repentis is an ascomycete fungus that causes tan spot of wheat. The disease has a worldwide distribution and can cause significant yield and quality losses in wheat production. The fungal pathogen is homothallic in nature, which means it can undergo sexual reproduction by selfing to produce pseudothecia on wheat stubble for seasonal survival. Since homothallism precludes the development of bi-parental fungal populations, no genetic linkage map has been developed for P. tritici-repentis for mapping and map-based cloning of fungal virulence genes. In this work, we created two heterothallic strains by deleting one of the mating type genes in each of two parental isolates 86-124 (race 2) and AR CrossB10 (a new race) and developed a bi-parental fungal population between them. The draft genome sequences of the two parental isolates were aligned to the Pt-1C-BFP reference sequence to mine single nucleotide polymorphisms (SNPs). A total of 225 SNP markers were developed for genotyping the entire population. Additionally, 75 simple sequence repeat, and two gene markers were also developed and used in the genotyping. The resulting linkage map consisted of 13 linkage groups spanning 5,075.83 cM in genetic distance. Because the parental isolate AR CrossB10 is a new race and produces Ptr ToxC, it was sequenced using long-read sequencing platforms and de novo assembled into contigs. The majority of the contigs were further anchored into chromosomes with the aid of the linkage maps. The whole genome comparison of AR CrossB10 to the reference genome of M4 revealed a few chromosomal rearrangements. The genetic linkage map and the new AR CrossB10 genome sequence are valuable tools for gene cloning in P. tritici-repentis.

Dissection and physical mapping of wheat chromosome 7B by inducing meiotic recombination with its homoeologues in Aegilops speltoides and Thinopyrum elongatum.

KEY MESSAGE: We constructed a homoeologous recombination-based bin map of wheat chromosome 7B, providing a unique physical framework for further study of chromosome 7B and its homoeologues in wheat and its relatives. Homoeologous recombination leads to the dissection and diversification of the wheat genome. Advances in genome sequencing and genotyping have dramatically improved the efficacy and throughput of homoeologous recombination-based genome studies and alien introgression in wheat and its relatives. In this study, we aimed to physically dissect and map wheat chromosome 7B by inducing meiotic recombination of chromosome 7B with its homoeologues 7E in Thinopyrum elongatum and 7S in Aegilops speltoides. The special genotypes, which were double monosomic for chromosomes 7B' + 7E' or 7B' + 7S' and homozygous for the ph1b mutant, were produced to enhance 7B - 7E and 7B - 7S recombination. Chromosome-specific DNA markers were developed and used to pre-screen the large recombination populations for 7B - 7E and 7B - 7S recombinants. The DNA marker-mediated preselections were verified by fluorescent genomic in situ hybridization (GISH). In total, 29 7B - 7E and 61 7B - 7S recombinants and multiple chromosome aberrations were recovered and delineated by GISH and the wheat 90 K SNP assay. Integrated GISH and SNP analysis of the recombinants physically mapped the recombination breakpoints and partitioned wheat chromosome 7B into 44 bins with 523 SNPs assigned within. A composite bin map was constructed for chromosome 7B, showing the bin size and physical distribution of SNPs. This provides a unique physical framework for further study of chromosome 7B and its homoeologues. In addition, the 7B - 7E and 7B - 7S recombinants extend the genetic variability of wheat chromosome 7B and represent useful germplasm for wheat breeding. Thereby, this genomics-enabled chromosome engineering approach facilitates wheat genome study and enriches the gene pool of wheat improvement.

Partitioning and physical mapping of wheat chromosome 3B and its homoeologue 3E in Thinopyrum elongatum by inducing homoeologous recombination.

KEY MESSAGE: We performed homoeologous recombination-based partitioning and physical mapping of wheat chromosome 3B and Th. elongatum chromosome 3E, providing a unique physical framework of this homoeologous pair for genome studies. The wheat (Triticum aestivum, 2n = 6x = 42, AABBDD) and Thinopyrum elongatum (2n = 2x = 14, EE) genomes can be differentiated from each other by fluorescent genomic in situ hybridization (FGISH) as well as molecular markers. This has facilitated homoeologous recombination-based partitioning and engineering of their genomes for physical mapping and alien introgression. Here, we constructed a special wheat genotype, which was double monosomic for wheat chromosome 3B and Th. elongatum chromosome 3E and homozygous for the ph1b mutant, to induce 3B-3E homoeologous recombination. Totally, 81 3B-3E recombinants were recovered and detected in the primary, secondary, and tertiary homoeologous recombination cycles by FGISH. Comparing to the primary recombination, the secondary and tertiary recombination shifted toward the proximal regions due to the increase in homology between the pairing partners. The 3B-3E recombinants were genotyped by high-throughput wheat 90-K single nucleotide polymorphism (SNP) arrays and their recombination breakpoints physically mapped based on the FGISH patterns and SNP results. The 3B-3E recombination physically partitioned chromosome 3B into 38 bins, and 429 SNPs were assigned to the distinct bins. Integrative analysis of FGISH and SNP results led to the construction of a composite bin map for chromosome 3B. Additionally, we developed 22 SNP-derived semi-thermal asymmetric reverse PCR markers specific for chromosome 3E and constructed a comparative map of homoeologous chromosomes 3E, 3B, 3A, and 3D. In summary, this work provides a unique physical framework for further studies of the 3B-3E homoeologous pair and diversifies the wheat genome for wheat improvement.

Molecular cytogenetic and genomic analyses reveal new insights into the origin of the wheat B genome.

KEY MESSAGE: This work pinpointed the goatgrass chromosomal segment in the wheat B genome using modern cytogenetic and genomic technologies, and provided novel insights into the origin of the wheat B genome. Wheat is a typical allopolyploid with three homoeologous subgenomes (A, B, and D). The donors of the subgenomes A and D had been identified, but not for the subgenome B. The goatgrass Aegilops speltoides (genome SS) has been controversially considered a possible candidate for the donor of the wheat B genome. However, the relationship of the Ae. speltoides S genome with the wheat B genome remains largely obscure. The present study assessed the homology of the B and S genomes using an integrative cytogenetic and genomic approach, and revealed the contribution of Ae. speltoides to the origin of the wheat B genome. We discovered noticeable homology between wheat chromosome 1B and Ae. speltoides chromosome 1S, but not between other chromosomes in the B and S genomes. An Ae. speltoides-originated segment spanning a genomic region of approximately 10.46 Mb was detected on the long arm of wheat chromosome 1B (1BL). The Ae. speltoides-originated segment on 1BL was found to co-evolve with the rest of the B genome. Evidently, Ae. speltoides had been involved in the origin of the wheat B genome, but should not be considered an exclusive donor of this genome. The wheat B genome might have a polyphyletic origin with multiple ancestors involved, including Ae. speltoides. These novel findings will facilitate genome studies in wheat and other polyploids.

Mechanism of N-Acylthiourea-mediated activation of human histone deacetylase 8 (HDAC8) at molecular and cellular levels.

We reported previously that an N-acylthiourea derivative (TM-2-51) serves as a potent and isozyme-selective activator for human histone deacetylase 8 (HDAC8). To probe the molecular mechanism of the enzyme activation, we performed a detailed account of the steady-state kinetics, thermodynamics, molecular modeling, and cell biology studies. The steady-state kinetic data revealed that TM-2-51 binds to HDAC8 at two sites in a positive cooperative manner. Isothermal titration calorimetric and molecular modeling data conformed to the two-site binding model of the enzyme-activator complex. We evaluated the efficacy of TM-2-51 on SH-SY5Y and BE(2)-C neuroblastoma cells, wherein the HDAC8 expression has been correlated with cellular malignancy. Whereas TM-2-51 selectively induced cell growth inhibition and apoptosis in SH-SY5Y cells, it showed no such effects in BE(2)-C cells, and this discriminatory feature appears to be encoded in the p53 genotype of the above cells. Our mechanistic and cellular studies on HDAC8 activation have the potential to provide insight into the development of novel anticancer drugs.

RNAseq reveals weed-induced PIF3-like as a candidate target to manipulate weed stress response in soybean.

Weeds reduce yield in soybeans (Glycine max) through incompletely defined mechanisms. The effects of weeds on the soybean transcriptome were evaluated in field conditions during four separate growing seasons. RNASeq data were collected from six biological samples of soybeans growing with or without weeds. Weed species and the methods to maintain weed-free controls varied between years to mitigate treatment effects, and to allow detection of general soybean weed responses. Soybean plants were not visibly nutrient- or water-stressed. We identified 55 consistently downregulated genes in weedy plots. Many of the downregulated genes were heat shock genes. Fourteen genes were consistently upregulated. Several transcription factors including a PHYTOCHROME INTERACTING FACTOR 3-like gene (PIF3) were included among the upregulated genes. Gene set enrichment analysis indicated roles for increased oxidative stress and jasmonic acid signaling responses during weed stress. The relationship of this weed-induced PIF3 gene to genes involved in shade avoidance responses in Arabidopsis provide evidence that this gene may be important in the response of soybean to weeds. These results suggest that the weed-induced PIF3 gene will be a target for manipulating weed tolerance in soybean.

Evaluation of a Pyrenophora teres f. teres mapping population reveals multiple independent interactions with a region of barley chromosome 6H.

The necrotrophic fungal pathogen Pyrenophora teres f. teres causes the foliar disease net form net blotch (NFNB) on barley. To investigate the genetics of virulence in the barley- P. teres f. teres pathosystem, we evaluated 118 progeny derived from a cross between the California isolates 15A and 6A on the barley lines Rika and Kombar, chosen based on their differential reactions to isolates 15A and 6A for NFNB disease. Genetic maps generated with SNP, SSR, and AFLP markers were scanned for quantitative trait loci (QTL) associated with virulence in P. teres f. teres. Loci underlying two major QTL, VR1 and VR2, were associated with virulence on Rika barley, accounting for 35% and 20% of the disease reaction type variation, respectively. Two different loci, VK1 and VK2, were shown to underlie two major QTL associated with virulence on Kombar barley accounting for 26% and 19% of the disease reaction type variation, respectively. Progeny isolates harboring VK1, VK2, or VR2 alone were inoculated onto a Rika×Kombar recombinant inbred line mapping population and the susceptibility induced by each pathogen genotype corresponded to the same region on barley chromosome 6H as that identified for the parental isolates 15A and 6A. The data presented here indicate that the P. teres f. teres - barley interaction can at least partially be explained by pathogen-produced necrotrophic effectors (NEs) that interact with dominant barley susceptibility genes resulting in NE triggered susceptibility (NETS).

Proteomics unite traditional toxicological assessment methods to evaluate the toxicity of iron oxide nanoparticles.

Iron oxide nanoparticles (IONPs) are the first generation of nanomaterials approved by the Food and Drug Administration for use as imaging agents and for the treatment of iron deficiency in chronic kidney disease. However, several IONPs-based imaging agents have been withdrawn because of toxic effects and the poor understanding of the underlying mechanisms. This study aimed to evaluate IONPs toxicity and to elucidate the underlying mechanism after intravenous administration in rats. Seven-week-old rats were intravenously administered IONPs at doses of 0, 10, 30, and 90 mg/kg body weight for 14 consecutive days. Toxicity and molecular perturbations were evaluated using traditional toxicological assessment methods and proteomics approaches, respectively. The administration of 90 mg/kg IONPs induced mild toxic effects, including abnormal clinical signs, lower body weight gain, changes in serum biochemical and hematological parameters, and increased organ coefficients in the spleen, liver, heart, and kidneys. Toxicokinetics, tissue distribution, histopathological, and transmission electron microscopy analyses revealed that the spleen was the primary organ for IONPs elimination from the systemic circulation and that the macrophage lysosomes were the main organelles of IONPs accumulation after intravenous administration. We identified 197 upregulated and 75 downregulated proteins in the spleen following IONPs administration by proteomics. Mechanically, the AKT/mTOR/TFEB signaling pathway facilitated autophagy and lysosomal activation in splenic macrophages. This is the first study to elucidate the mechanism of IONPs toxicity by combining proteomics with traditional methods for toxicity assessment.

Impacts of reference selection on the assembly of suspicious coronavirus genome.

The pandemic caused by SARS-CoV-2 has had a significant impact on the whole world. In a theory of the origin of SARS-CoV-2, pangolins are considered as a potential intermediate host. To assemble the genome of suspicious coronavirus (CoV) found in pangolins, SARS-CoV-2 was used as a reference in most of the previous studies, implicitly assuming the pangolin CoV and SARS-CoV-2 are the closest neighbors in evolution. However, this assumption may not be true. We investigated how the choice of reference genome affected the resulting CoV genome assembly. We explored various representative CoVs as the reference genome, and found significant differences in the resulting assemblies. The assembly obtained using RaTG13 as a reference showed better statistics in total length, N50, and pairwise distance reconstruction (PDR) scores than the assembly guided by SARS-CoV-2, indicating that RaTG13 may be a better reference. Therefore, RaTG13 should also be considered as a reference for assembling suspicious CoV found in pangolins and other potential intermediate hosts.

A tool for calculating binding-site residues on proteins from PDB structures.

BACKGROUND: In the research on protein functional sites, researchers often need to identify binding-site residues on a protein. A commonly used strategy is to find a complex structure from the Protein Data Bank (PDB) that consists of the protein of interest and its interacting partner(s) and calculate binding-site residues based on the complex structure. However, since a protein may participate in multiple interactions, the binding-site residues calculated based on one complex structure usually do not reveal all binding sites on a protein. Thus, this requires researchers to find all PDB complexes that contain the protein of interest and combine the binding-site information gleaned from them. This process is very time-consuming. Especially, combing binding-site information obtained from different PDB structures requires tedious work to align protein sequences. The process becomes overwhelmingly difficult when researchers have a large set of proteins to analyze, which is usually the case in practice. RESULTS: In this study, we have developed a tool for calculating binding-site residues on proteins, TCBRP http://yanbioinformatics.cs.usu.edu:8080/ppbindingsubmit. For an input protein, TCBRP can quickly find all binding-site residues on the protein by automatically combining the information obtained from all PDB structures that consist of the protein of interest. Additionally, TCBRP presents the binding-site residues in different categories according to the interaction type. TCBRP also allows researchers to set the definition of binding-site residues. CONCLUSION: The developed tool is very useful for the research on protein binding site analysis and prediction.

Chlorpyrifos induces delayed cytotoxicity after withdrawal in primary hippocampal neurons through extracellular signal-regulated kinase inhibition.

In this study, the delayed effect and related mechanism after chlorpyrifos (CPF) withdrawal was studied in primary rat hippocampal neurons. The results showed that 10 muM CPF induced no detectable cytotoxicity during 96 h continuous exposure while its withdrawal after 48 h exposure induced evident cytotoxicity, as indexed by decreased methyl thiazolyl tetrazolium (MTT) metabolism, increased loss of neurons immunostained by neuron-specific enolase (NSE) antibody, and the increased terminal deoxynucleotidyl transferase-mediated deoxyuridine triphosphate nick end labeling (TUNEL) positive cell rate in the following 24 h and 48 h incubation in the absence of CPF. Extracellular signal-related kinase (ERK)1/2 activation by phosphorylation was observed and persisted during CPF exposure. However, CPF withdrawal after 48 h exposure led to inhibition of ERK1/2 phosphorylation. Carbacol and nerve growth factor (NGF), which are ERK1/2 activators, protected the neurons after CPF withdrawal, while atropine and PD98059, which are ERK1/2 inhibitors, exacerbated the cytotoxicity, indicating the involvement of inhibition of ERK1/2 phosphorylation in CPF-induced delayed cytotoxicity. In conclusion, CPF withdrawal after exposure induced delayed cytotoxicity in cultured neurons. Inhibition of ERK1/2 phosphorylation was found to be related to the delayed cytotoxicity. This finding may provide a new insight into the toxicological mechanism of organophosphorus pesticides, especially chronic organophosphate-induced neuropsychiatric disorder characterized by delayed occurrence.

Chronic organophosphate (OP)-induced neuropsychiatric disorder is a withdrawal syndrome.

Chronic organophosphate-induced neuropsychiatric disorder is a less well-characterized syndrome, which is usually delay-occurred, persists long and is similar to the symptom of cholinergic deficit, its mechanism is unclear. The characteristics of chronic organophosphate-induced neuropsychiatric disorder are somewhat opposite to the direct action of OP pesticide, since withdrawal effect is usually opposite to the original effect of a drug, hypothesis that chronic organophosphate-induced neuropsychiatric disorder is a kind of withdrawal syndrome is suggested.

Secondary formation damage of low-pressure layer during commingled production in multilayered tight gas reservoirs.

This paper experimentally investigates fluid back-flow behavior and formation damage during commingled production in multilayered tight gas reservoirs. The development of fluid back-flow in commingled tight gas reservoirs was simulated using a newly designed experimental platform. The results indicate that when there is a pressure difference between different layers during commingled production from tight gas reservoir, water produced from the high-pressure layer will invade the low-pressure layer along with gas back-flow and will accumulate in the near-wellbore area. This will lead to an increase in water saturation and a decline in permeability in the low-pressure layer and result in a significant reduction in ultimate recovery. The outcomes of these experiments demonstrate that as well as the formation damage caused by the working fluid during drilling and fracturing, "Secondary Formation Damage" also occurs during commingled production in multilayered tight gas reservoirs. This secondary formation damage mainly occurs in the near-wellbore area of low-pressure layers and is more severe with greater proximity to the wellbore. Through further experimentation to assess the factors influencing secondary formation damage, it is shown that the degree of secondary formation damage increases with decreasing original formation pressure, original water saturation, and permeability in the lower-pressure layer.

An enrichment method for mapping ambiguous reads to the reference genome for NGS analysis.

Mapping short reads to a reference genome is an essential step in many next-generation sequencing (NGS) analyses. In plants with large genomes, a large fraction of the reads can align to multiple locations of the genome with equally good alignment scores. How to map these ambiguous reads to the genome is a challenging problem with big impacts on the downstream analysis. Traditionally, the default method is to assign an ambiguous read randomly to one of the many potential locations. In this study, we explore two alternative methods that are based on the hypothesis that the possibility of an ambiguous read being generated by a location is proportional to the total number of reads produced by that location: (1) the enrichment method that assigns an ambiguous read to the location that has produced the most reads among all the potential locations, (2) the probability method that assigns an ambiguous read to a location based on a probability proportional to the number of reads the location produces. We systematically compared the performance of the proposed methods with that of the default random method. Our results showed that the enrichment method produced better results than the default random method and the probability method in the discovery of single nucleotide polymorphisms (SNPs). Not only did it produce more SNP markers, but it also produced SNP markers with better quality, which was demonstrated using multiple mainstay genomic analyses, including genome-wide association studies (GWAS), minor allele distribution, population structure, and genomic prediction.

Identification of deleterious non-synonymous single nucleotide polymorphisms using sequence-derived information.

BACKGROUND: As the number of non-synonymous single nucleotide polymorphisms (nsSNPs), also known as single amino acid polymorphisms (SAPs), increases rapidly, computational methods that can distinguish disease-causing SAPs from neutral SAPs are needed. Many methods have been developed to distinguish disease-causing SAPs based on both structural and sequence features of the mutation point. One limitation of these methods is that they are not applicable to the cases where protein structures are not available. In this study, we explore the feasibility of classifying SAPs into disease-causing and neutral mutations using only information derived from protein sequence. RESULTS: We compiled a set of 686 features that were derived from protein sequence. For each feature, the distance between the wild-type residue and mutant-type residue was computed. Then a greedy approach was used to select the features that were useful for the classification of SAPs. 10 features were selected. Using the selected features, a decision tree method can achieve 82.6% overall accuracy with 0.607 Matthews Correlation Coefficient (MCC) in cross-validation. When tested on an independent set that was not seen by the method during the training and feature selection, the decision tree method achieves 82.6% overall accuracy with 0.604 MCC. We also evaluated the proposed method on all SAPs obtained from the Swiss-Prot, the method achieves 0.42 MCC with 73.2% overall accuracy. This method allows users to make reliable predictions when protein structures are not available. Different from previous studies, in which only a small set of features were arbitrarily chosen and considered, here we used an automated method to systematically discover useful features from a large set of features well-annotated in public databases. CONCLUSION: The proposed method is a useful tool for the classification of SAPs, especially, when the structure of the protein is not available.

Discrimination of outer membrane proteins with improved performance.

BACKGROUND: Outer membrane proteins (OMPs) perform diverse functional roles in Gram-negative bacteria. Identification of outer membrane proteins is an important task. RESULTS: This paper presents a method for distinguishing outer membrane proteins (OMPs) from non-OMPs (that is, globular proteins and inner membrane proteins (IMPs)). First, we calculated the average residue compositions of OMPs, globular proteins and IMPs separately using a training set. Then for each protein from the test set, its distances to the three groups were calculated based on residue composition using a weighted Euclidean distance (WED) approach. Proteins from the test set were classified into OMP versus non-OMP classes based on the least distance. The proposed method can distinguish between OMPs and non-OMPs with 91.0% accuracy and 0.639 Matthews correlation coefficient (MCC). We then improved the method by including homologous sequences into the calculation of residue composition and using a feature-selection method to select the single residue and di-peptides that were useful for OMP prediction. The final method achieves an accuracy of 96.8% with 0.859 MCC. In direct comparisons, the proposed method outperforms previously published methods. CONCLUSION: The proposed method can identify OMPs with improved performance. It will be very helpful to the discovery of OMPs in a genome scale.

Characterization of protein-protein interfaces.

We analyze the characteristics of protein-protein interfaces using the largest datasets available from the Protein Data Bank (PDB). We start with a comparison of interfaces with protein cores and non-interface surfaces. The results show that interfaces differ from protein cores and non-interface surfaces in residue composition, sequence entropy, and secondary structure. Since interfaces, protein cores, and non-interface surfaces have different solvent accessibilities, it is important to investigate whether the observed differences are due to the differences in solvent accessibility or differences in functionality. We separate out the effect of solvent accessibility by comparing interfaces with a set of residues having the same solvent accessibility as the interfaces. This strategy reveals residue distribution propensities that are not observable by comparing interfaces with protein cores and non-interface surfaces. Our conclusions are that there are larger numbers of hydrophobic residues, particularly aromatic residues, in interfaces, and the interactions apparently favored in interfaces include the opposite charge pairs and hydrophobic pairs. Surprisingly, Pro-Trp pairs are over represented in interfaces, presumably because of favorable geometries. The analysis is repeated using three datasets having different constraints on sequence similarity and structure quality. Consistent results are obtained across these datasets. We have also investigated separately the characteristics of heteromeric interfaces and homomeric interfaces.