The muscle research community, in collaboration with the GO Consortium, has completed an initiative to greatly expand the muscle biology representation in the GO biological process and cellular component ontologies. The work focused on improving and adding terms urgently needed for current priority areas in research.
The main focus of the work was skeletal muscle, with specific consideration given to the processes of muscle contraction, muscle plasticity, muscle development and regeneration; and to the sarcomere and membrane-delimited cell compartments. Our aims were to update the existing structure to reflect current knowledge, and to resolve in an accommodating manner, the ambiguities in the language used by the muscle community. This collaborative effort drew on the knowledge of an extensive community of muscle experts, and resulted in the addition of 159 new terms and the improvement of 57 existing terms.
These different areas of muscle biology were addressed to support specific research needs. In the following text, the motivation for the changes and the details of each set of changes are described.
There are two different possible biological meanings of the commonly used phrase 'muscle plasticity', such that plasticity could be either the quality of adaptability or the process of adaptation. In ontology development it is essential to be clear about which term represents which process; and to ensure that the language is unambiguous, whilst still reflecting community usage. The existing muscle plasticity term was ambiguously named, risking incorrect use in annotation or text mining. However, as the term was clearly defined to describe the process of adaptation, we were able to resolve the problem by renaming the term muscle adaptation (leaving muscle plasticity as a related synonym, to help researchers find the term). This action resolved the ambiguity, but accommodated the common uses of the word 'plasticity' in domain literature by retaining the word as a searchable related synonym.
There are many stimuli that bring about muscle adaptation. Musculo-skeletal adaptability studies include examination of a muscle's response to joint immobilization, spinal cord injury, electrical stimulation, chronic stretch, exercise-induced injury, and microgravity. Adaptive events that occur in muscle fibers and associated structures (motor neurons and capillaries) include atrophy, hypertrophy, and hyperplasia, and these involve alterations in regulatory mechanisms, contractile properties, fiber-type compositions, and metabolic capacities. Previously these processes were not covered in the GO as the term muscle plasticity (Figure ) had no more specific child terms. During the editing work, terms covering these important sub-processes have been included (Figure ).
Figure 1 Muscle plasticity GO node. As an example, the process 'muscle plasticity' is shown before (Panel A) and after (Panel B) our modifications. Previously, the process of muscle plasticity had no specific child terms, therefore all annotations of the gene (more ...)
Using these new more granular terms, biologists will be able to annotate gene products in more detail. Prior to our work, if a gene was thought to be involved in muscle atrophy, the user had only the option of annotating directly to the general term 'muscle plasticity'. As a result of our contribution, the ontology now includes child terms representing muscle atrophy, hypertrophy and hyperplasia. It also includes generic regulation terms under each of these processes, and under these regulation terms the actual regulatory processes are grouped. To illustrate the advantage of creation of these new terms the muscle experts have contributed some annotations that could previously only be made to the general muscle plasticity term (Figure ) and that can now be distributed amongst the more specific child terms for much greater reasoning power (Figure ). This small amount of annotation clearly shows how much better this enhanced structure is for distinguishing sets of gene products involved in the various processes that contribute to the general process of muscle adaptation. Though we have shown only a handful of gene products, it can easily be imagined how much more powerful the system will be in automated analysis of the activity of thousands of gene products, as is the case in a microarray experiment. For example, once the relevant gene products are fully annotated, it will be possible to detect by microarray experiment those stimuli that upregulate hundreds of genes involved in muscle hypertrophy, whilst barely affecting the regulation of genes involved in muscle atrophy.
This new set of terms should assist in the annotation of gene products involved in the control of muscle fiber-type diversity, providing potential new targets for the treatment and prevention of different disorders ranging from metabolic to neuromuscular diseases, for example Type 2 diabetes and muscular dystrophy [9
]. We have explained this example of muscle plasticity very fully to illustrate the motivation behind our ontology development work. The work carried out on other areas of the ontology will bring similar benefits with regard to other critical areas of research, and we describe these pieces of work somewhat more briefly below with reference to the areas of research that they are intended to support.
The definition of the term muscle contraction, which previously existed in the GO, has been considerably improved and all of its descendants have been reorganized. The new structure represents several forms of muscle contraction and their relationships with the various types of muscle. To reflect this, there is also a greatly expanded set of terms describing the different contractile capacity of muscle. Striated muscle contracts and relaxes in short, intense bursts, whereas smooth muscle sustains longer or even near-permanent contractions. This difference was captured by the creation of is_a children, phasic smooth muscle contraction and tonic smooth muscle contraction, under the parent term smooth muscle contraction. Since the process of smooth muscle contraction varies with the anatomical location of muscles, terms such as vascular muscle contraction and gastro-intestinal muscle contraction were also created.
Muscle contraction is actively regulated by a series of events, for which appropriate regulation terms have been added. These include several processes such as cross-bridge formation, cross-bridge cycling, and filament sliding, which are necessary for force generation during muscle contraction. Multiple molecular components, such as sarcoplasmic proteins, have a role in regulating the muscle contraction. For instance mutations in several Z-disc proteins in the sarcomere, that are important for the cross-linking of thin filaments and transmission of force generated by the myofilaments, have been shown to cause cardiomyopathies and/or muscular dystrophies [10
]. To accommodate this, a definition of the sarcomeric Z-disc
has been added to the component ontology and extended to include recently discovered novel attributes associated with this structure, such as mechanosensation and mechanotransduction, thereby allowing users to view the Z-disc not so much as a static, but now as a flexible structure with important implications for signal transduction as well [11
The previously described process of muscle plasticity is closely linked with, and highly dependent on, calcium metabolism and transport, as muscles use calcium ions as their main regulatory and signaling molecule. Therefore, calcium ion-dependent processes control the properties of the mechanisms of contraction and relaxation in different types of muscle fibers [12
]. The sarcoplasmic reticulum (SR) is a sub-compartment of the endoplasmic reticulum (ER) and is molecularly specialized for calcium release, uptake, and storage and for the contraction-relaxation cycle in skeletal muscle fibers [13
]. Recognizing the importance of this, we focused part of our work on improving the existing terms describing sarcoplasmic reticulum and its role in regulating the calcium ion-dependent processes. Terms such regulation of skeletal muscle contraction by calcium ion signaling
and regulation of skeletal muscle contraction via modulation of calcium ion sensitivity of myofibril
were added as part_of children of muscle contraction
. In addition, the sarcoplasmic reticulum compartment and its components are covered by an expanded hierarchy of terms. Whilst the term sarcoplasmic reticulum
pre-existed in the GO (Figure ) we have been able to add many new child terms (Figure ). This allows the gene products whose locations of action could previously only be categorized loosely using the single sarcoplasmic reticulum
term (Figure ) to be categorized in far more detail (Figure ). We give this example in detail with annotations to indicate how the additions to the cellular component ontology provide similar benefits to those in the biological processes ontology, previously illustrated by use of the muscle plasticity
example. The new child terms in this case include longitudinal sarcoplasmic reticulum
, terminal cisterna
, terminal cisterna lumen
, free sarcoplasmic reticulum membrane
, and junctional sarcoplasmic reticulum membrane
. These new GO terms will aid our understanding of normal muscle processes and muscle pathological conditions such as dystrophinopathies, Brody's disease, and malignant hyperthermia. These have been shown to be due to alterations in calcium ion-dependent ion channel activities [12
Figure 2 Sarcoplasmic reticulum GO node. As an example, the cellular component 'sarcoplasmic reticulum' is shown before (Panel A) and after (Panel B) the modifications described in this paper. Previously, the term sarcoplasmic reticulum had no specific child terms, (more ...)
Muscles can be divided into striated and smooth types. Smooth muscle or 'involuntary muscle' is found within structures such as the oesophagus, stomach, intestines, bronchi, uterus, and blood vessels. Unlike skeletal muscle, smooth muscle is not under conscious control. Cardiac and skeletal muscles are striated in that they contain sarcomeres and are packed into highly regular arrangements of bundles.
Skeletal muscles are further divided into two subtypes, slow-twitch and fast-twitch muscle, depending on their contractile capacity. The biology of these two muscle types is key in current research, so we worked to represent it correctly as part of the biological process ontology. Improvements were made to the representation of these areas, to ensure that the usage of the words 'skeletal' and 'striated' was representative of that in the community. Importantly, these terms were also cross-checked by a cardiovascular physiology community group, whose ontology development effort took place at the same time, and which also touched on voluntary/involuntary muscle processes (David Hill, personal communication).
Muscle Development and Regeneration
Myofibers, the functional unit of skeletal muscle, are long cylindrical multinucleated cells that vary in their morphological, biochemical, and physiological properties. They are derived from myoblasts: cells committed to the skeletal muscle lineage. Upon fusion, myoblasts form myotubes, which are further remodeled into myofibers [14
]. The skeletal muscle development
subtree has been enhanced during our work with a new hierarchy of terms describing myoblast
, and myofiber development
, and the mechanisms of their regulation. To accommodate recent data, a distinction was introduced between head and trunk muscle development [15
Many terms have been added to cover the process of cell regeneration and its regulation in skeletal muscle tissue. These include terms such as satellite cell activation involved in skeletal muscle regeneration
and satellite cell compartment self renewal involved in skeletal muscle regeneration
. Satellite cell processes are considered particularly important, since their activation is involved in muscle regeneration. Satellite cell proliferation, differentiation, and self-renewal are essential for proper myofiber turnover; an ongoing process that maintains proper muscle tissue viability [16
]. Moreover, in adult skeletal muscle, the self-renewing capacity of satellite cells contributes to muscle growth and adaptation [17
]. Skeletal muscle is capable of complete regeneration due to the presence of stem cells that reside in skeletal muscle and non-muscle stem cell populations. However, in severe myopathic diseases such as Duchenne Muscular Dystrophy, this regenerative capacity is exhausted [18
]. We have attempted to support research into these areas by addition of the relevant terms.