Iterative orthology prediction uncovers new mitochondrial proteins and identifies C12orf62 as the human ortholog of COX14, a protein involved in the assembly of cytochrome c oxidase

BACKGROUND: Orthology is a central tenet of comparative genomics and ortholog identification is instrumental to protein function prediction. Major advances have been made to determine orthology relations among a set of homologous proteins. However, they depend on the comparison of individual sequences and do not take into account divergent orthologs. RESULTS: We have developed an iterative orthology prediction method, Ortho-Profile, that uses reciprocal best hits at the level of sequence profiles to infer orthology. It increases ortholog detection by 20% compared to sequence-to-sequence comparisons. Ortho-Profile predicts 598 human orthologs of mitochondrial proteins from Saccharomyces cerevisiae and Schizosaccharomyces pombe with 94% accuracy. Of these, 181 were not known to localize to mitochondria in mammals. Among the predictions of the Ortho-Profile method are 11 human cytochrome c oxidase (COX) assembly proteins that are implicated in mitochondrial function and disease. Their co-expression patterns, experimentally verified subcellular localization, and co-purification with human COX-associated proteins support these predictions. For the human gene C12orf62, the ortholog of S. cerevisiae COX14, we specifically confirm its role in negative regulation of the translation of cytochrome c oxidase. CONCLUSIONS: Divergent homologs can often only be detected by comparing sequence profiles and profile-based hidden Markov models. The Ortho-Profile method takes advantage of these techniques in the quest for orthologs

Association between plasma metabolites and gene expression profiles in five porcine endocrine tissues

Background: Endocrine tissues play a fundamental role in maintaining homeostasis of plasma metabolites such as non-esterified fatty acids and glucose, the levels of which reflect the energy balance or the health status of animals. However, the relationship between the transcriptome of endocrine tissues and plasma metabolites has been poorly studied. Methods: We determined the blood levels of 12 plasma metabolites in 27 pigs belonging to five breeds, each breed consisting of both females and males. The transcriptome of five endocrine tissues i.e. hypothalamus, adenohypophysis, thyroid gland, gonads and backfat tissues from 16 out of the 27 pigs was also determined. Sex and breed effects on the 12 plasma metabolites were investigated and associations between genes expressed in the five endocrine tissues and the 12 plasma metabolites measured were analyzed. A probeset was defined as a quantitative trait transcript (QTT) when its association with a particular metabolic trait achieved a nominal P value < 0.01. Results: A larger than expected number of QTT was found for non-esterified fatty acids and alanine aminotransferase in at least two tissues. The associations were highly tissue-specific. The QTT within the tissues were divided into co-expression network modules enriched for genes in Kyoto Encyclopedia of Genes and Genomes or gene ontology categories that are related to the physiological functions of the corresponding tissues. We also explored a multi-tissue co-expression network using QTT for non-esterified fatty acids from the five tissues and found that a module, enriched in hypothalamus QTT, was positioned at the centre of the entire multi-tissue network. Conclusions: These results emphasize the relationships between endocrine tissues and plasma metabolites in terms of gene expression. Highly tissue-specific association patterns suggest that candidate genes or gene pathways should be investigated in the context of specific tissues

C7orf30 specifically associates with the large subunit of the mitochondrial ribosome and is involved in translation

In a comparative genomics study for mitochondrial ribosome-associated proteins, we identified C7orf30, the human homolog of the plant protein iojap. Gene order conservation among bacteria and the observation that iojap orthologs cannot be transferred between bacterial species predict this protein to be associated with the mitochondrial ribosome. Here, we show colocalization of C7orf30 with the large subunit of the mitochondrial ribosome using isokinetic sucrose gradient and 2D Blue Native polyacrylamide gel electrophoresis (BN-PAGE) analysis. We co-purified C7orf30 with proteins of the large subunit, and not with proteins of the small subunit, supporting interaction that is specific to the large mitoribosomal complex. Consistent with this physical association, a mitochondrial translation assay reveals negative effects of C7orf30 siRNA knock-down on mitochondrial gene expression. Based on our data we propose that C7orf30 is involved in ribosomal large subunit function. Sequencing the gene in 35 patients with impaired mitochondrial translation did not reveal disease-causing mutations in C7orf30

Retrograde traffic in the biosynthetic-secretory route

In the biosynthetic-secretory route from the rough endoplasmic reticulum, across the pre-Golgi intermediate compartments, the Golgi apparatus stacks, trans Golgi network, and post-Golgi organelles, anterograde transport is accompanied and counterbalanced by retrograde traffic of both membranes and contents. In the physiologic dynamics of cells, retrograde flow is necessary for retrieval of molecules that escaped from their compartments of function, for keeping the compartments’ balances, and maintenance of the functional integrities of organelles and compartments along the secretory route, for repeated use of molecules, and molecule repair. Internalized molecules may be transported in retrograde direction along certain sections of the secretory route, and compartments and machineries of the secretory pathway may be misused by toxins. An important example is the toxin of Shigella dysenteriae, which has been shown to travel from the cell surface across endosomes, and the Golgi apparatus en route to the endoplasmic reticulum, and the cytosol, where it exerts its deleterious effects. Most importantly in medical research, knowledge about the retrograde cellular pathways is increasingly being utilized for the development of strategies for targeted delivery of drugs to the interior of cells. Multiple details about the molecular transport machineries involved in retrograde traffic are known; a high number of the molecular constituents have been characterized, and the complicated fine structural architectures of the compartments involved become more and more visible. However, multiple contradictions exist, and already established traffic models again are in question by contradictory results obtained with diverse cell systems, and/or different techniques. Additional problems arise by the fact that the conditions used in the experimental protocols frequently do not reflect the physiologic situations of the cells. Regular and pathologic situations often are intermingled, and experimental treatments by themselves change cell organizations. This review addresses physiologic and pathologic situations, tries to correlate results obtained by different cell biologic techniques, and asks questions, which may be the basis and starting point for further investigations

Rab proteins specify motorized vesicle transport.

Contains fulltext : 71292.pdf (publisher's version ) (Open Access)Small GTPases of the Rab-family are key regulators of intracellular membrane traffic. These proteins constantly cycle between an 'active' GTP-bound and 'inactive' GDP-bound state. In their GTP-bound conformation Rab proteins can engage in complex formation with so called effector proteins. It is at this level that the control of membrane transport is exerted. To date more than 60 Rab-family members, including isoforms, are recognized. To this family also belongs the Golgi-localized Rab6. In the past three different isoforms of this protein were identified: Rab6A, Rab6A'(generated by alternative splicing of a homologues but distinct exon within the Rab6 gene), and a brain specific isoform, Rab6B. Rab6A' is the isoform regulating the entire retrograde pathway from late endosomes to ER, whereas Rab6A seems dispensable for this route. The role of Rab6B is still ill-defined and therefore the main focus of this study. Studies using GFP-Rab6B in neuronal cells revealed the bi-directional movement of Rab6B positive structures in neurites of these cells, possibly belonging to the post-Golgi compartment. This latter finding was corroborated with a tsVSVG-assay, which localized Rab6B on vesicles moving from the Golgi towards the plasma membrane. Furthermore we also found co-localization of Rab6B with vesicles containing internalized GPI-anchored proteins. A regulatory role for Rab6B in the internalization of these proteins can therefore be anticipated. To learn more about the molecular environment of Rab6B we searched for novel Rab6B interacting proteins. Of the newly identified Rab6B interactors two were analyzed in more detail, namely Bicaudal-D1 and DYNLRB1. Whereas Bicaudal-D1 provides an indirect binding of Rab6B to the dynein/dynactin motor protein complex, DYNLRB1 assures direct binding. Dynein/dynactin is the main microtubule based motor protein complex responsible for long range retrograde transport. Based on our findings we expect an important role for Rab6B in regulating this process which, especially in neurons, is important in cell survival and viability.RU Radboud Universiteit Nijmegen, 29 mei 2008Promotor : Wieringa, B. Co-promotor : Fransen, J.A.M.151 p

A review on the role of salivary MUC5B in oral health

Background: The salivary glycoprotein MUC5B plays a versatile role in maintaining oral health. It contributes to lubrication, pellicle formation, antimicrobial defense, and water retention, and its glycans are an important nutrient for oral bacteria. This review aimed to describe the role of MUC5B in oral health and examine changes in its levels and composition in cases of hyposalivation and xerostomia. Highlight: In cases of hyposalivation, the reduction of total salivary MUC5B levels and MUC5B glycosylation patterns due to Sjögren's syndrome (SS) and medication intake appeared insignificantly limited. In patients with SS, xerostomia was related to reduced MUC5B levels at the anterior tongue. In cases of xerostomia, MUC5B glycosylation might be reduced, yet other factors such as total protein concentration, MUC7 levels and glycosylation, and salivary spinnbarkeit are involved. In contrast to SS- and medication-induced hyposalivation, radiotherapy in the head and neck region leads to a bona fide reduction in salivary MUC5B levels. Conclusion: Our findings suggest that MUC5B levels are clearly impaired in hyposalivation and xerostomia related to radiotherapy in the head and neck region versus those related to SS and medication intake. A reduction in glycosylation in the case of dry mouth appears associated with MUC5B and MUC7 as well as other factors

A role for the Rab6B Bicaudal-D1 interaction in retrograde transport in neuronal cells.

Contains fulltext : 53424.pdf (publisher's version ) (Closed access)The Rab6 subfamily of small GTPases consists of three different isoforms: Rab6A, Rab6A' and Rab6B. Both Rab6A and Rab6A' are ubiquitously expressed whereas Rab6B is predominantly expressed in brain. Recent studies have shown that Rab6A' is the isoform regulating the retrograde transport from late endosomes via the Golgi to the ER and in the transition from anaphase to metaphase during mitosis. Since the role of Rab6B is still ill defined, we set out to characterize its intracellular environment and dynamic behavior. In a Y-2H search for novel Rab6 interacting proteins, we identified Bicaudal-D1, a large coiled-coil protein known to bind to the dynein/dynactin complex and previously shown to be a binding partner for Rab6A/Rab6A'. Co-immunoprecipitation studies and pull down assays confirmed that Bicaudal-D1 also interacts with Rab6B in its active form. Using confocal laser scanning microscopy it was established that Rab6B and Bicaudal-D1 co-localize at the Golgi and vesicles that align along microtubules. Furthermore, both proteins co-localized with dynein in neurites of SK-N-SH cells. Live cell imaging revealed bi-directional movement of EGFP-Rab6B structures in SK-N-SH neurites. We conclude from our data that the brain-specific Rab6B via Bicaudal-D1 is linked to the dynein/dynactin complex, suggesting a regulatory role for Rab6B in the retrograde transport of cargo in neuronal cells