Developmental changes of the protein repertoire in the rat auditory brainstem: a comparative proteomics approach in the superior olivary complex and the inferior colliculus with DIGE and iTRAQ

Proteome Analysis of PC12 Cells Reveals Alterations in Translation Regulation and Actin Signaling Induced by Clozapine

Although antipsychotics are routinely used in the treatment of schizophrenia for the last decades, their precise mechanism of action is still unclear. In this study, we investigated changes in the PC12 cells’ proteome under the influence of clozapine, risperidone, and haloperidol to identify protein pathways regulated by antipsychotics. Analysis of the protein profiles in two time points: after 12 and 24 h of incubation with drugs revealed significant alterations in 510 proteins. Further canonical pathway analysis revealed an inhibition of ciliary trophic factor signaling after treatment with haloperidol and showed a decrease in acute phase response signaling in the risperidone group. Interestingly, all tested drugs have caused changes in PC12 proteome which correspond to inhibition of cytokines: tumor necrosis factor (TNF) and transforming growth factor beta 1 (TGF-β1). We also found that the 12-h incubation with clozapine caused up-regulation of protein kinase A signaling and translation machinery. After 24 h of treatment with clozapine, the inhibition of the actin cytoskeleton signaling and Rho proteins signaling was revealed. The obtained results suggest that the mammalian target of rapamycin complex 1 (mTORC1) and 2 (mTORC2) play a central role in the signal transduction of clozapine.

Considerable differences between auditory medulla, auditory midbrain, and hippocampal synapses during sustained high-frequency stimulation: Exceptional vesicle replenishment restricted to sound localization circuit

Reliable synaptic transmission is essential for interneuronal communication. Synaptic inputs to auditory brainstem neurons, particularly those involved in sound localization, are characterized by resilience during sustained activity and temporal precision in the sub-millisecond range. Both features are obtained by synchronous release of a high number of synaptic vesicles following a single action potential. Here, we compare transmission behavior of three heterogeneous types of inputs in the auditory midbrain and medulla. The first terminate in the central inferior colliculus (ICc) and are glutamatergic (activated from the lateral lemniscus, LL). The medullary inputs terminate in the lateral superior olive (LSO) and are glutamatergic (from the cochlear nuclear complex, CN) or glycinergic (from the medial nucleus of the trapezoid body, MNTB). LSO neurons are the first to integrate binaural information and compute interaural level differences, whereas ICc neurons receive information from almost all auditory brainstem nuclei and construct an initial auditory image used for reflexive behavior. We hypothesized that CN-LSO and MNTB-LSO inputs are more resilient to synaptic fatigue during sustained stimulation than LL-ICc inputs. To test the hypothesis, we performed whole-cell patch-clamp recordings in acute brainstem slices of juvenile mice. We investigated the synaptic performance during prolonged periods of high-frequency stimulation (60 s, up to 200 Hz) and assessed several features, e.g. depression, recovery, latency, temporal precision, quantal size and content, readily releasable pool size, release probability, and replenishment rate. Overall, LL-ICc inputs performed less robustly and temporally precisely than CN-LSO and MNTB-LSO inputs. When stimulated at ≥50 Hz, the former depressed completely within a few seconds. In contrast, CN-LSO and MNTB-LSO inputs transmitted faithfully up to 200 Hz, indicative of very efficient replenishment mechanisms. LSO inputs also displayed considerably lower latency jitter than LL-ICc inputs. The latter behaved similarly to two types of input in the hippocampus for which we performed a meta-analysis. Mechanistically, the high-fidelity behavior of LSO inputs, particularly MNTB-LSO synapses, is based on exceptional release properties not present at auditory midbrain or hippocampal inputs. We conclude that robustness and temporal precision are hallmarks of auditory synapses in the medullary brainstem. These key features are less eminent at higher stations, such as the ICc, and they are also absent outside the central auditory system, namely the hippocampal formation.

Poor transcript-protein correlation in the brain: negatively correlating gene products reveal neuronal polarity as a potential cause

Transcription, translation, and turnover of transcripts and proteins are essential for cellular function. The contribution of those factors to protein levels is under debate, as transcript levels and cognate protein levels do not necessarily correlate due to regulation of translation and protein turnover. Here we propose neuronal polarity as a third factor that is particularly evident in the CNS, leading to considerable distances between somata and axon terminals. Consequently, transcript levels may negatively correlate with cognate protein levels in CNS regions, i.e., transcript and protein levels behave reciprocally. To test this hypothesis, we performed an integrative inter-omics study and analyzed three interconnected rat auditory brainstem regions (cochlear nuclear complex, CN; superior olivary complex, SOC; inferior colliculus, IC) and the rest of the brain as a reference. We obtained transcript and protein sets in these regions of interest (ROIs) by DNA microarrays and label-free mass spectrometry, and performed principal component and correlation analyses. We found 508 transcript|protein pairs and detected poor to moderate transcript|protein correlation in all ROIs, as evidenced by coefficients of determination from 0.34 to 0.54. We identified 57-80 negatively correlating gene products in the ROIs and intensively analyzed four of them for which the correlation was poorest. Three cognate proteins (Slc6a11, Syngr1, Tppp) were synaptic and hence candidates for a negative correlation because of protein transport into axon terminals. Thus, we systematically analyzed the negatively correlating gene products. Gene ontology analyses revealed overrepresented transport/synapse-related proteins, supporting our hypothesis. We present 30 synapse/transport-related proteins with poor transcript|protein correlation. In conclusion, our analyses support that protein transport in polar cells is a third factor that influences the protein level and, thereby, the transcript|protein correlation. OPEN SCIENCE BADGES: This article has received a badge for *Open Materials* and *Open Data* because it provided all relevant information to reproduce the study in the manuscript and because it made the data publicly available. The data can be accessed at https://osf.io/ha28n/. The complete Open Science Disclosure form for this article can be found at the end of the article. More information about the Open Practices badges can be found at https://cos.io/our-services/open-science-badges/.

Synaptic reliability and temporal precision are achieved via high quantal content and effective replenishment: auditory brainstem versus hippocampus

KEY POINTS

Auditory brainstem neurons involved in sound source localization are equipped with several morphological and molecular features that enable them to compute interaural level and time differences. As sound source localization works continually, synaptic transmission between these neurons should be reliable and temporally precise, even during sustained periods of high-frequency activity. Using patch-clamp recordings in acute brain slices, we compared synaptic reliability and temporal precision in the seconds-minute range between auditory and two types of hippocampal synapses; the latter are less confronted with temporally precise high-frequency transmission than the auditory ones. We found striking differences in synaptic properties (e.g. continually high quantal content) that allow auditory synapses to reliably release vesicles at much higher rate than their hippocampal counterparts. Thus, they are indefatigable and also in a position to transfer information with exquisite temporal precision and their performance appears to be supported by very efficient replenishment mechanisms.

ABSTRACT

At early stations of the auditory pathway, information is encoded by precise signal timing and rate. Auditory synapses must maintain the relative timing of events with submillisecond precision even during sustained and high-frequency stimulation. In non-auditory brain regions, e.g. telencephalic ones, synapses are activated at considerably lower frequencies. Central to understanding the heterogeneity of synaptic systems is the elucidation of the physical, chemical and biological factors that determine synapse performance. In this study, we used slice recordings from three synapse types in the mouse auditory brainstem and hippocampus. Whereas the auditory brainstem nuclei experience high-frequency activity in vivo, the hippocampal circuits are activated at much lower frequencies. We challenged the synapses with sustained high-frequency stimulation (up to 200 Hz for 60 s) and found significant performance differences. Our results show that auditory brainstem synapses differ considerably from their hippocampal counterparts in several aspects, namely resistance to synaptic fatigue, low failure rate and exquisite temporal precision. Their high-fidelity performance supports the functional demands and appears to be due to the large size of the readily releasable pool and a high release probability, which together result in a high quantal content. In conjunction with very efficient vesicle replenishment mechanisms, these properties provide extremely rapid and temporally precise signalling required for neuronal communication at early stations of the auditory system, even during sustained activation in the minute range.

Multi-omics analysis on the pathogenicity of Enterobacter cloacae ENHKU01 isolated from sewage outfalls along the Ningbo coastline

BACKGROUND

The acquisition of iron is important for the pathogenicity of bacteria and blood. Three different culture environments (Fe stimulation, blood agar plate and normal plate) were used to stimulate Enterobacter cloacae, and their respective pathogenicities were compared at the proteomic, mRNA and metabolomic levels.

METHODS

2D-DIGE combined with MALDI-TOF-MS/MS, RT-PCR and ¹H NMR were used to analyze the differential expression levels of proteins, mRNA and metabolites.

RESULTS

A total of 109 proteins were identified by 2D-DIGE and mass spectrometry after pairwise comparison within three culture environments, clustered into 3 classes and 183 functional categories, which were involved in 23 pathways. Based on the 2D-DIGE results, multiple proteins were selected for verification by mRNA expression. These results confirmed that most of the proteins were regulated at the transcriptional level. Thirty-eight metabolites were detected by NMR, which correlated with the differentially expressed proteins under different treatment conditions.

CONCLUSIONS

The results show that culture in a blood agar plate and a suitable concentration of iron promote the pathogenicity of E. cloacae and that high iron concentrations may have adverse effects on growth and iron uptake and utilization by E. cloacae.

Characterization and comparison of proteomes of albino sea cucumber Apostichopus japonicus (Selenka) by iTRAQ analysis

Sea cucumber is a commercially important marine organism in China. Of the different colored varieties sold in China, albino sea cucumber has the greatest appeal among consumers. Identification of factors contributing to albinism in sea cucumber is therefore likely to provide a scientific basis for improving the cultivability of these strains. In this study, two-dimensional liquid chromatography-tandem mass spectrometry coupled with isobaric tags for relative and absolute quantification labeling was used for the first time to quantitatively define the proteome of sea cucumbers and reveal proteomic characteristics unique to albino sea cucumbers. A total of 549 proteins were identified and quantified in albino sea cucumber and the functional annotations of 485 proteins have been exhibited based on COG database. Compared with green sea cucumber, 12 proteins were identified as differentially expressed in the intestine and 16 proteins in the body wall of albino sea cucumber. Among them, 5 proteins were up-regulated in the intestine and 8 proteins were down-regulated in body wall. Gene ontology annotations of these differentially expressed proteins consisted mostly of 'biological process'. The large number of differentially expressed proteins identified here should be highly useful in further elucidating the mechanisms underlying albinism in sea cucumber.

Transcriptional maturation of the mouse auditory forebrain

Background

The maturation of the brain involves the coordinated expression of thousands of genes, proteins and regulatory elements over time. In sensory pathways, gene expression profiles are modified by age and sensory experience in a manner that differs between brain regions and cell types. In the auditory system of altricial animals, neuronal activity increases markedly after the opening of the ear canals, initiating events that culminate in the maturation of auditory circuitry in the brain. This window provides a unique opportunity to study how gene expression patterns are modified by the onset of sensory experience through maturity. As a tool for capturing these features, next-generation sequencing of total RNA (RNAseq) has tremendous utility, because the entire transcriptome can be screened to index expression of any gene. To date, whole transcriptome profiles have not been generated for any central auditory structure in any species at any age. In the present study, RNAseq was used to profile two regions of the mouse auditory forebrain (A1, primary auditory cortex; MG, medial geniculate) at key stages of postnatal development (P7, P14, P21, adult) before and after the onset of hearing (~P12). Hierarchical clustering, differential expression, and functional geneset enrichment analyses (GSEA) were used to profile the expression patterns of all genes. Selected genesets related to neurotransmission, developmental plasticity, critical periods and brain structure were highlighted. An accessible repository of the entire dataset was also constructed that permits extraction and screening of all data from the global through single-gene levels. To our knowledge, this is the first whole transcriptome sequencing study of the forebrain of any mammalian sensory system. Although the data are most relevant for the auditory system, they are generally applicable to forebrain structures in the visual and somatosensory systems, as well.

Results

The main findings were: (1) Global gene expression patterns were tightly clustered by postnatal age and brain region; (2) comparing A1 and MG, the total numbers of differentially expressed genes were comparable from P7 to P21, then dropped to nearly half by adulthood; (3) comparing successive age groups, the greatest numbers of differentially expressed genes were found between P7 and P14 in both regions, followed by a steady decline in numbers with age; (4) maturational trajectories in expression levels varied at the single gene level (increasing, decreasing, static, other); (5) between regions, the profiles of single genes were often asymmetric; (6) GSEA revealed that genesets related to neural activity and plasticity were typically upregulated from P7 to adult, while those related to structure tended to be downregulated; (7) GSEA and pathways analysis of selected functional networks were not predictive of expression patterns in the auditory forebrain for all genes, reflecting regional specificity at the single gene level.

Conclusions

Gene expression in the auditory forebrain during postnatal development is in constant flux and becomes increasingly stable with age. Maturational changes are evident at the global through single gene levels. Transcriptome profiles in A1 and MG are distinct at all ages, and differ from other brain regions. The database generated by this study provides a rich foundation for the identification of novel developmental biomarkers, functional gene pathways, and targeted studies of postnatal maturation in the auditory forebrain.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1709-8) contains supplementary material, which is available to authorized users.

The proteome profiles of the olfactory bulb of juvenile, adult and aged rats - an ontogenetic study

Background

In this study, we searched for proteins that change their expression in the olfactory bulb (oB) of rats during ontogenesis. Up to now, protein expression differences in the developing animal are not fully understood. Our investigation focused on the question whether specific proteins exist which are only expressed during different development stages. This might lead to a better characterization of the microenvironment and to a better determination of factors and candidates that influence the differentiation of neuronal progenitor cells.

Results

After analyzing the samples by two-dimensional polyacrylamide gel electrophoresis (2DE) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS), it could be shown that the number of expressed proteins differs depending on the developmental stages. Especially members of the functional classes, like proteins of biosynthesis, regulatory proteins and structural proteins, show the highest differential expression in the stages of development analyzed.

Conclusion

In this study, quantitative changes in the expression of proteins in the oB at different developmental stages (postnatal days (P) 7, 90 and 637) could be observed. Furthermore, the expression of many proteins was found at specific developmental stages. It was possible to identify these proteins which are involved in processes like support of cell migration and differentiation.

Electronic supplementary material

The online version of this article (doi:10.1186/s12953-014-0058-x) contains supplementary material, which is available to authorized users.