Using a 3D virtual muscle model to link gene expression changes during myogenesis to protein spatial location in muscle

Colonisation of Meat by Escherichia coli O157:H7: Investigating Bacterial Tropism with Respect to the Different Types of Skeletal Muscles, Subtypes of Myofibres, and Postmortem Time

Escherichia coli O157:H7 is an enterohaemorrhagic E. coli (EHEC) responsible for serious diseases, especially pediatric, and of great concern for the meat industry. Meat contamination by EHEC occurs at slaughtering, especially at dehiding stage, where bacteria can be transferred from hides to carcasses. The skeletal muscle tissues comprise four major types of myofibres, which differ in their contraction velocity and metabolism. Myofibres are surrounded by the extracellular matrix (ECM). Adhesion of E. coli O157:H7 to meat was investigated considering well-defined types of skeletal muscle and their constituent myofibres as well as postmortem changes in muscle, using fluorescence microscopy and immunohistochemical analyses. By analysing the adhesion of E. coli O157:H7 to model oxidative (soleus) and glycolytic [extensor digitorum longus (EDL)] skeletal muscles, it first appeared that differential adhesion occurred at the surface of these extreme skeletal muscle types. At a cellular level, bacterial adhesion appeared to occur essentially at the ECM. Considering the different constituent myofibres of types I, IIA, IIX and IIB, no significant differences were observed for adhering bacteria. However, bacterial adhesion to the ECM was significantly influenced by postmortem structural modifications of muscle tissues. By providing information on spatial localisation of E. coli O157:H7 on meat, this investigation clearly demonstrated their ability to adhere to skeletal muscle, especially at the ECM, which consequently resulted in their heterogeneous distribution in meat. As discussed, these new findings should help in reassessing and mitigating the risk of contamination of meat, the food chain and ultimately human infection by EHEC.

Progesterone signalling in broiler skeletal muscle is associated with divergent feed efficiency

Background

We contrast the pectoralis muscle transcriptomes of broilers selected from within a single genetic line expressing divergent feed efficiency (FE) in an effort to improve our understanding of the mechanistic basis of FE.

Results

Application of a virtual muscle model to gene expression data pointed to a coordinated reduction in slow twitch muscle isoforms of the contractile apparatus (MYH15, TPM3, MYOZ2, TNNI1, MYL2, MYOM3, CSRP3, TNNT2), consistent with diminishment in associated slow machinery (myoglobin and phospholamban) in the high FE animals. These data are in line with the repeated transition from red slow to white fast muscle fibres observed in agricultural species selected on mass and FE. Surprisingly, we found that the expression of 699 genes encoding the broiler mitoproteome is modestly–but significantly–biased towards the high FE group, suggesting a slightly elevated mitochondrial content. This is contrary to expectation based on the slow muscle isoform data and theoretical physiological capacity arguments. Reassuringly, the extreme 40 most DE genes can successfully cluster the 12 individuals into the appropriate FE treatment group. Functional groups contained in this DE gene list include metabolic proteins (including opposing patterns of CA3 and CA4), mitochondrial proteins (CKMT1A), oxidative status (SEPP1, HIG2A) and cholesterol homeostasis (APOA1, INSIG1). We applied a differential network method (Regulatory Impact Factors) whose aim is to use patterns of differential co-expression to detect regulatory molecules transcriptionally rewired between the groups. This analysis clearly points to alterations in progesterone signalling (via the receptor PGR) as the major driver. We show the progesterone receptor localises to the mitochondria in a quail muscle cell line.

Conclusions

Progesterone is sometimes used in the cattle industry in exogenous hormone mixes that lead to a ~20% increase in FE. Because the progesterone receptor can localise to avian mitochondria, our data continue to point to muscle mitochondrial metabolism as an important component of the phenotypic expression of variation in broiler FE.

Electronic supplementary material

The online version of this article (doi:10.1186/s12918-017-0396-2) contains supplementary material, which is available to authorized users.

An Always Correlated gene expression landscape for ovine skeletal muscle, lessons learnt from comparison with an "equivalent" bovine landscape

Background

We have recently described a method for the construction of an informative gene expression correlation landscape for a single tissue, longissimus muscle (LM) of cattle, using a small number (less than a hundred) of diverse samples. Does this approach facilitate interspecies comparison of networks?

Findings

Using gene expression datasets from LM samples from a single postnatal time point for high and low muscling sheep, and from a developmental time course (prenatal to postnatal) for normal sheep and sheep exhibiting the Callipyge muscling phenotype gene expression correlations were calculated across subsets of the data comparable to the bovine analysis. An “Always Correlated” gene expression landscape was constructed by integrating the correlations from the subsets of data and was compared to the equivalent landscape for bovine LM muscle. Whilst at the high level apparently equivalent modules were identified in the two species, at the detailed level overlap between genes in the equivalent modules was limited and generally not significant. Indeed, only 395 genes and 18 edges were in common between the two landscapes.

Conclusions

Since it is unlikely that the equivalent muscles of two closely related species are as different as this analysis suggests, within tissue gene expression correlations appear to be very sensitive to the samples chosen for their construction, compounded by the different platforms used. Thus users need to be very cautious in interpretation of the differences. In future experiments, attention will be required to ensure equivalent experimental designs and use cross-species gene expression platform to enable the identification of true differences between different species.

Phosphoinositide 3-kinase (PI3K(p110alpha)) directly regulates key components of the Z-disc and cardiac structure

Maintenance of cardiac structure and Z-disc signaling are key factors responsible for protecting the heart in a setting of stress, but how these processes are regulated is not well defined. We recently demonstrated that PI3K(p110α) protects the heart against myocardial infarction. The aim of this study was to determine whether PI3K(p110α) directly regulates components of the Z-disc and cardiac structure. To address this question, a unique three-dimensional virtual muscle model was applied to gene expression data from transgenic mice with increased or decreased PI3K(p110α) activity under basal conditions (sham) and in a setting of myocardial infarction to display the location of structural proteins. Key findings from this analysis were then validated experimentally. The three-dimensional virtual muscle model visually highlighted reciprocally regulated transcripts associated with PI3K activation that encoded key components of the Z-disc and costamere, including melusin. Studies were performed to assess whether PI3K and melusin interact in the heart. Here, we identify a novel melusin-PI3K interaction that generates lipid kinase activity. The direct impact of PI3K(p110α) on myocyte structure was assessed by treating neonatal rat ventricular myocytes with PI3K(p110α) inhibitors and examining the myofiber morphology of hearts from PI3K transgenic mice. Results demonstrate that PI3K is critical for myofiber maturation and Z-disc alignment. In summary, PI3K regulates the expression of genes essential for cardiac structure and Z-disc signaling, interacts with melusin, and is critical for Z-disc alignment.