Human-Soybean Allergies: Elucidation of the Seed Proteome and Comprehensive Protein-Protein Interaction Prediction.

The soybean crop, Glycine max (L.) Merr., is consumed by humans, Homo sapiens, worldwide. While the respective bodies of literature and -omics data for each of these organisms are extensive, comparatively few studies investigate the molecular biological processes occurring between the two. We are interested in elucidating the network of protein-protein interactions (PPIs) involved in human-soybean allergies. To this end, we leverage state-of-the-art sequence-based PPI predictors amenable to predicting the enormous comprehensive interactome between human and soybean. A network-based analytical approach is proposed, leveraging similar interaction profiles to identify candidate allergens and proteins involved in the allergy response. Interestingly, the predicted interactome can be explored from two complementary perspectives: which soybean proteins are predicted to interact with specific human proteins and which human proteins are predicted to interact with specific soybean proteins. A total of eight proteins (six specific to the human proteome and two to the soy proteome) have been identified and supported by the literature to be involved in human health, specifically related to immunological and neurological pathways. This study, beyond generating the most comprehensive human-soybean interactome to date, elucidated a soybean seed interactome and identified several proteins putatively consequential to human health.

Identifying new variation at the J locus, previously identified as e6, in long juvenile 'Paranagoiana' soybean.

KEY MESSAGE: A previously identified soybean maturity locus, E6, is discovered to be J, with the long juvenile allele in Paranagoiana now deemed j-x. Soybean grown at latitudes of ~20° or lower can produce lower grain yields due to the short days. This limitation can be overcome by using the long juvenile trait (LJ) which delays flowering under short day conditions. Two LJ loci have been mapped to the same location on Gm04, J and E6. The objective of this research was to investigate the e6 allele in 'Paranagoiana' and determine if E6 and J are the same locus or linked loci. KASP markers showed that e6 lines did not have the j-1 allele of LJ PI 159925. A population fixed for E1 but segregating for E6, with e6 introgressed from Paranagoiana, showed single gene control for flowering and maturity under short days. Sequencing Glyma.04G050200, the J gene, with long amplification Taq found that the e6 line 'Paranagoiana' contains a Ty1-copia retrotransposon of ~10,000 bp, inserted within exon 4. PCR amplification of the cDNA of Glyma.04G050200 also showed differences between the mRNA sequences (presence of insertion in j-x). Hence, we conclude that the loci E6 and J are one locus and deem this new variation found in Paranagoiana as j-x.

The Ethylene Oxide Product Test of Sterility: Limitations and Interpretation of Results.

The ethylene oxide (EO) product test of sterility (ToS) can be conducted to comply with ANSI/AAMI/ISO 11135:2014 for the generation of data to demonstrate the appropriateness of the biological indicator (BI) that is used to develop and qualify the EO sterilization process. Clause D.8.6 of 11135 provides an option to perform a sublethal EO process, followed by conducting a product ToS, performing sterility testing of BIs from the process challenge device, and comparing the test results. Certain limitations for the EO product ToS should be considered when conducting studies that feature the use of this test, in order to support compliance with this requirement. Limitations for any sterility test include sample size, testing frequency, detection sensitivity, and/or the potential for false-positive/false-negative results, each of which must be recognized and well understood in order to support compliance with the standard. In addition, the experimental design of any study featuring the use of a sterility test should be carefully developed to ensure the generation of scientifically sound results and conclusions to support the study objective.

IκB kinase regulation of the TPL-2/ERK MAPK pathway.

Nuclear factor-κB (NF-κB) and mitogen-activated protein kinase (MAPK) activation play central roles in the induction of gene expression in innate immune cells following pathogen recognition. TPL-2 (tumor progression locus 2) is the MAP 3-kinase component of an ERK-1/2 (extracellular signal-regulated kinase 1/2) MAPK pathway activated by Toll-like receptor and tumor necrosis factor receptor family stimulation. In this review, we discuss results obtained from our laboratory and others that show that TPL-2 signaling function is directly controlled by the inhibitor of NF-κB (IκB) kinase (IKK) complex. Significantly, this means that IKK controls both NF-κB and ERK activation. TPL-2 is stoichiometrically complexed with the NF-κB inhibitory protein, NF-κB1 p105, and the ubiquitin-binding protein ABIN-2, both of which are required to maintain TPL-2 protein stability. Binding to p105 also prevents TPL-2 from phosphorylating MEK (MAPK/ERK kinase), its downstream target. Agonist stimulation releases TPL-2 from p105-inhibition by IKK-mediated phosphorylation of p105, which triggers degradation of p105 by the proteasome. This facilitates TPL-2 phosphorylation of MEK, in addition to liberating p105-associated Rel subunits to translocate into the nucleus. We also examine evidence that TPL-2 is critical for the induction of inflammation and may play a role in development and/or progression of certain types of cancer. Finally, we consider the potential of TPL-2 as an anti-inflammatory drug target for treatment of certain types of inflammatory disease and cancer.

Prediction of protein domain boundaries from inverse covariances.

It has been known even since relatively few structures had been solved that longer protein chains often contain multiple domains, which may fold separately and play the role of reusable functional modules found in many contexts. In many structural biology tasks, in particular structure prediction, it is of great use to be able to identify domains within the structure and analyze these regions separately. However, when using sequence data alone this task has proven exceptionally difficult, with relatively little improvement over the naive method of choosing boundaries based on size distributions of observed domains. The recent significant improvement in contact prediction provides a new source of information for domain prediction. We test several methods for using this information including a kernel smoothing-based approach and methods based on building alpha-carbon models and compare performance with a length-based predictor, a homology search method and four published sequence-based predictors: DOMCUT, DomPRO, DLP-SVM, and SCOOBY-DOmain. We show that the kernel-smoothing method is significantly better than the other ab initio predictors when both single-domain and multidomain targets are considered and is not significantly different to the homology-based method. Considering only multidomain targets the kernel-smoothing method outperforms all of the published methods except DLP-SVM. The kernel smoothing method therefore represents a potentially useful improvement to ab initio domain prediction.

Prediction of protein contacts from correlated sequence substitutions.

Recent work has led to a substantial improvement in the accuracy of predictions of contacts between amino acids using evolutionary information derived from multiple sequence alignments. Where large numbers of diverse sequence relatives are available and can be aligned to the sequence of a protein of unknown structure, it is now possible to generate high-resolution models without recourse to the structure of a template. In this review, we describe these exciting new techniques and critically assess the state of the art in contact prediction in light of them. We discuss areas for immediate research and development as well as potential future developments.

FOXRED1, encoding an FAD-dependent oxidoreductase complex-I-specific molecular chaperone, is mutated in infantile-onset mitochondrial encephalopathy.

Complex I is the first and largest enzyme in the respiratory chain and is located in the inner mitochondrial membrane. Complex I deficiency is the most commonly reported mitochondrial disorder presenting in childhood, but the molecular basis of most cases remains elusive. We describe a patient with complex I deficiency caused by mutation of the molecular chaperone FOXRED1. A combined homozygosity mapping and bioinformatics approach in a consanguineous Iranian-Jewish pedigree led to the identification of a homozygous mutation in FOXRED1 in a child who presented with infantile-onset encephalomyopathy. Silencing of FOXRED1 in human fibroblasts resulted in reduced complex I steady-state levels and activity, while lentiviral-mediated FOXRED1 transgene expression rescued complex I deficiency in the patient fibroblasts. This FAD-dependent oxidoreductase, which has never previously been associated with human disease, is now shown to be a complex I-specific molecular chaperone. The discovery of the c.1054C>T; p.R352W mutation in the FOXRED1 gene is a further contribution towards resolving the complex puzzle of the genetic basis of human mitochondrial disease.

A nonsense mutation in COQ9 causes autosomal-recessive neonatal-onset primary coenzyme Q10 deficiency: a potentially treatable form of mitochondrial disease.

Coenzyme Q(10) is a mobile lipophilic electron carrier located in the inner mitochondrial membrane. Defects of coenzyme Q(10) biosynthesis represent one of the few treatable mitochondrial diseases. We genotyped a patient with primary coenzyme Q(10) deficiency who presented with neonatal lactic acidosis and later developed multisytem disease including intractable seizures, global developmental delay, hypertrophic cardiomyopathy, and renal tubular dysfunction. Cultured skin fibroblasts from the patient had a coenzyme Q(10) biosynthetic rate of 11% of normal controls and accumulated an abnormal metabolite that we believe to be a biosynthetic intermediate. In view of the rarity of coenzyme Q(10) deficiency, we hypothesized that the disease-causing gene might lie in a region of ancestral homozygosity by descent. Data from an Illumina HumanHap550 array were analyzed with BeadStudio software. Sixteen regions of homozygosity >1.5 Mb were identified in the affected infant. Two of these regions included the loci of two of 16 candidate genes implicated in human coenzyme Q(10) biosynthesis. Sequence analysis demonstrated a homozygous stop mutation affecting a highly conserved residue of COQ9, leading to the truncation of 75 amino acids. Site-directed mutagenesis targeting the equivalent residue in the yeast Saccharomyces cerevisiae abolished respiratory growth.

Kearns-Sayre syndrome caused by defective R1/p53R2 assembly.

BACKGROUND: Mutations in RRM2B encoding ribonucleotide reductase (RNR) p53R2 subunit usually cause paediatric-onset mitochondrial disease associated with mitochondrial DNA (mtDNA) depletion. The importance of RNR dysfunction in adult mitochondrial disease is unclear. OBJECTIVE: To report the RRM2B mutation frequency in adults with multiple mtDNA deletions and examine RNR assembly in a patient with Kearns-Sayre syndrome (KSS) caused by two novel RRM2B mutations. METHODS: 50 adult patients with multiple mtDNA deletions in skeletal muscle were studied. DNA sequencing of RRM2B was performed in patients without mutations in mtDNA maintenance genes POLG and C10orf2. RNR protein was studied using western blot and Blue-native polyacrylamide gel electrophoresis (BN-PAGE). RESULTS: Four per cent (two unrelated cases) of this adult cohort harboured RRM2B mutations. Patient 1 had KSS and two novel missense mutations: c.122G→A; p.Arg41Gln and c.391G→A; p.Glu131Lys. BN-PAGE demonstrated reduced heterotetrameric R1/p53R2 RNR levels compared with controls, despite normal steady-state p53R2 levels on western blot, suggesting failed assembly of functional RNR as a potential disease mechanism. Patient 2 had late-onset progressive external ophthalmoplegia and fatigue. A heterozygous deletion c.253_255delGAG; p.Glu85del was identified. Muscle histology in both cases showed significant numbers of necrotic muscle fibres, possibly indicating enhanced apoptotic cell death. CONCLUSION: These data indicate that 4% of adult mitochondrial disease with multiple deletions is caused by RNR dysfunction. KSS has not previously been linked to a nuclear gene defect. Evidence that disease pathogenesis may be caused by defective RNR assembly is given. RRM2B screening should be considered early in the differential diagnosis of adults with multiple mtDNA deletions.

Parametric Release of Moist Heat Sterilized Products: History and Current State.

The sterility test has been utilized for many years to formally support the sterile release of products terminally sterilized by moist heat and other sterilization modalities. It is well-known that the sterility test is severely limited in providing a meaningful scientific and statistical basis to support the sterility of finished products. Accordingly, parametric release was developed as a sterility assurance release program that defines critical manufacturing process and sterilization control parameters that are essential for sterile product release, thereby eliminating the use of the sterility test. This article examines the limitations and shortcomings of the sterility test and reviews the findings from a case study to illustrate the risks associated with the overreliance on this test for the disposition of sterile products. The history of parametric release of products terminally sterilized with moist heat is presented with a summary of the current status, including a listing of global regulatory standards and guidances along with a discussion of applicable results from an industry survey of moist heat sterilization practice. This article is intended to be the initial step to establish a basic understanding of the parametric release concept and practices that can be leveraged as a baseline for future promotion and expanded implementation.

De novo backbone scaffolds for protein design.

In recent years, there have been significant advances in the field of computational protein design including the successful computational design of enzymes based on backbone scaffolds from experimentally solved structures. It is likely that large-scale sampling of protein backbone conformations will become necessary as further progress is made on more complicated systems. Removing the constraint of having to use scaffolds based on known protein backbones is a potential method of solving the problem. With this application in mind, we describe a method to systematically construct a large number of de novo backbone structures from idealized topological forms in a top-down hierarchical approach. The structural properties of these novel backbone scaffolds were analyzed and compared with a set of high-resolution experimental structures from the protein data bank (PDB). It was found that the Ramachandran plot distribution and relative gamma- and beta-turn frequencies were similar to those found in the PDB. The de novo scaffolds were sequence designed with RosettaDesign, and the energy distributions and amino acid compositions were comparable with the results for redesigned experimentally solved backbones.

pGenTHREADER and pDomTHREADER: new methods for improved protein fold recognition and superfamily discrimination.

MOTIVATION: Generation of structural models and recognition of homologous relationships for unannotated protein sequences are fundamental problems in bioinformatics. Improving the sensitivity and selectivity of methods designed for these two tasks therefore has downstream benefits for many other bioinformatics applications. RESULTS: We describe the latest implementation of the GenTHREADER method for structure prediction on a genomic scale. The method combines profile-profile alignments with secondary-structure specific gap-penalties, classic pair- and solvation potentials using a linear combination optimized with a regression SVM model. We find this combination significantly improves both detection of useful templates and accuracy of sequence-structure alignments relative to other competitive approaches. We further present a second implementation of the protocol designed for the task of discriminating superfamilies from one another. This method, pDomTHREADER, is the first to incorporate both sequence and structural data directly in this task and improves sensitivity and selectivity over the standard version of pGenTHREADER and three other standard methods for remote homology detection.

An automatic method for assessing structural importance of amino acid positions.

BACKGROUND: A great deal is known about the qualitative aspects of the sequence-structure relationship, for example that buried residues are usually more conserved between structurally similar homologues, but no attempts have been made to quantitate the relationship between evolutionary conservation at a sequence position and change to global tertiary structure. In this paper we demonstrate that the Spearman correlation between sequence and structural change is suitable for this purpose. RESULTS: Buried residues, bends, cysteines, prolines and leucines were significantly more likely to occupy positions highly correlated with structural change than expected by chance. Some buried residues were found to be less informative than expected, particularly residues involved in active sites and the binding of small molecules. CONCLUSION: The correlation-based method generates predictions of structural importance for superfamily positions which agree well with previous results of manual analyses, and may be of use in automated residue annotation piplines. A PERL script which implements the method is provided.

Harnessing QbD, Programming Languages, and Automation for Reproducible Biology.

Building robust manufacturing processes from biological components is a task that is highly complex and requires sophisticated tools to describe processes, inputs, and measurements and administrate management of knowledge, data, and materials. We argue that for bioengineering to fully access biological potential, it will require application of statistically designed experiments to derive detailed empirical models of underlying systems. This requires execution of large-scale structured experimentation for which laboratory automation is necessary. This requires development of expressive, high-level languages that allow reusability of protocols, characterization of their reliability, and a change in focus from implementation details to functional properties. We review recent developments in these areas and identify what we believe is an exciting trend that promises to revolutionize biotechnology.

Prediction of contacts from correlated sequence substitutions.

Recent work has led to a substantial improvement in the accuracy of predictions of contacts between amino acids using evolutionary information derived from multiple sequence alignments. Where large numbers of diverse sequence relatives are available and can be aligned to the sequence of a protein of unknown structure it is now possible to generate high-resolution models without recourse to the structure of a template. In this review we describe these exciting new techniques and critically assess the state-of-the-art in contact prediction in the light of these. While concentrating on methods, we also discuss applications to protein and RNA structure prediction as well as potential future developments.

COX10 mutations resulting in complex multisystem mitochondrial disease that remains stable into adulthood.

IMPORTANCE: Isolated cytochrome-c oxidase (COX) deficiency is one of the most frequent respiratory chain defects seen in human mitochondrial disease. Typically, patients present with severe neonatal multisystem disease and have an early fatal outcome. We describe an adult patient with isolated COX deficiency associated with a relatively mild clinical phenotype comprising myopathy; demyelinating neuropathy; premature ovarian failure; short stature; hearing loss; pigmentary maculopathy; and renal tubular dysfunction. OBSERVATIONS: Whole-exome sequencing detected 1 known pathogenic and 1 novel COX10 mutation: c.1007A>T; p.Asp336Val, previously associated with fatal infantile COX deficiency, and c.1015C>T; p.Arg339Trp. Muscle COX holoenzyme and subassemblies were undetectable on immunoblots of blue-native gels, whereas denaturing gels and immunocytochemistry showed reduced core subunit MTCO1. Heme absorption spectra revealed low heme aa3 compatible with heme A:farnesyltransferase deficiency due to COX10 dysfunction. Both mutations demonstrated respiratory deficiency in yeast, confirming pathogenicity. A COX10 protein model was used to predict the structural consequences of the novel Arg339Trp and all previously reported substitutions. CONCLUSIONS AND RELEVANCE: These findings establish that COX10 mutations cause adult mitochondrial disease. Nuclear modifiers, epigenetic phenomenon, and/or environmental factors may influence the disease phenotype caused by reduced COX activity and contribute to the variable clinical severity related to COX10 dysfunction.

Protein topology from predicted residue contacts.

Residue contacts predicted from correlated positions in a multiple sequence alignment are often sparse and uncertain. To some extent, these limitations in the data can be overcome by grouping the contacts by secondary structure elements and enumerating the possible packing arrangements of these elements in a combinatorial manner. Strong interactions appear frequently but inconsistent interactions are down-weighted and missing interactions up-weighted. The resulting improved consistency in the predicted interactions has allowed the method to be successfully applied to proteins up to 200 residues in length which is larger than any structure previously predicted using sequence data alone.

Analytic markovian rates for generalized protein structure evolution.

A general understanding of the complex phenomenon of protein evolution requires the accurate description of the constraints that define the sub-space of proteins with mutations that do not appreciably reduce the fitness of the organism. Such constraints can have multiple origins, in this work we present a model for constrained evolutionary trajectories represented by a markovian process throughout a set of protein-like structures artificially constructed to be topological intermediates between the structure of two natural occurring proteins. The number and type of intermediate steps defines how constrained the total evolutionary process is. By using a coarse-grained representation for the protein structures, we derive an analytic formulation of the transition rates between each of the intermediate structures. The results indicate that compact structures with a high number of hydrogen bonds are more probable and have a higher likelihood to arise during evolution. Knowledge of the transition rates allows for the study of complex evolutionary pathways represented by trajectories through a set of intermediate structures.

Structural constraints on the covariance matrix derived from multiple aligned protein sequences.

Residue contact predictions were calculated based on the mutual information observed between pairs of positions in large multiple protein sequence alignments. Where previously only the statistical properties of these data have been considered important, we introduce new measures to impose constraints that make the contact map more consistent with a three dimensional structure. These included global (bulk) properties and local secondary structure properties. The latter allowed the contact constraints to be employed at the level of filtering pairs of secondary structure contacts which led to a more efficient (lower-level) implementation in the PLATO structure prediction server. Where previously the measure of success with this method had been whether the correct fold was predicted in the top 10 ranked models, with the current implementation, our summary statistic is the number of correct folds included in the top 10 models--which is on average over 50 percent.