SNARE Dance

Abstract

There is little doubt that humans rely on vision as their primary sensory input. However, various studies indicate that audiovisual combinations of data presentation actually enhance the ability of the learner to comprehend the information. We present an example of a musical-biological interface that provides an audible demonstration of SNARE protein function in the process of macroautophagy.

Keywords: :

• SNARE protein
• protein targeting
• stress
• vacuole
• yeast

Introduction

Music is a universal language. A familiar arrangement of notes has the power to evoke a specific feeling or experience and can be used to introduce new concepts. The tangible components of a musical composition such as notes, dynamics, tempo, and instrumentation can be used to explain complex biological concepts such as transcription and translation. Music therefore can be a teaching tool. Biological processes are ubiquitous and music can be used not only to teach all ages and backgrounds about such processes, but also to engage and explore science using an auditory format. Such an approach could create an additional layer of information for and interpretation of pre-existing data such as protein sequences.¹ The main challenge of combining music and science is to balance the two components so that neither the musicality nor the scientific data are compromised in translation. Here, we describe the process of creating SNARE Dance, an orchestration depicting autophagosome biogenesis, using the Gene2Music program.

SNARE Dance focuses on three SNARE proteins and the transmembrane protein Atg9. In yeast, Atg9 is the only transmembrane protein that is required for autophagosome formation,² although Atg27, which is also an integral membrane protein, facilitates this process; fewer autophagosomes are formed in the absence of Atg27.^3,4 Unlike most Atg proteins, Atg9 is localized in multiple puncta in wild-type cells, one of these corresponding to the phagophore assembly site (PAS). Fluorescence microscopy analysis of Atg9 localization in an atg1^ts mutant suggests that this protein moves to the PAS from the peripheral peri-mitochondrial sites (referred to as Atg9 reservoirs).^5,6 Electron microscopy studies indicate that the peripheral sites correspond to tubulovesicular clusters (TVCs), and that an individual TVC may be converted into a phagophore.⁵

Movement of Atg9 to the TVCs is dependent on SNARE proteins.⁷ In an sso1Δ sso2^ts mutant, Atg9 accumulates in post-Golgi complex vesicles. Sso1/Sso2 are highly homologous plasma membrane syntaxins (SNAREs) that are involved in exocytosis. These proteins interact with the plasma membrane SNARE light chain Sec9, and a defect in the latter also blocks Atg9 delivery to the TVCs. Sec22 is a vesicle SNARE that plays a role in ER and Golgi transport; however, a sec22 mutation causes a defect in Atg9 transport to the TVC, suggesting that Sec22 may be the v-SNARE that directs Sso1/2-Sec9 to function in autophagy.

Based on these data, we chose Atg9, Sso1, Sec22 and Sec9 for conversion of their amino acid sequences into musical notes. The corresponding pieces were arranged together to simulate the “SNARE Dance.”

Results

Generation of musical scores and instrumentation for each protein

The amino acid sequences of Atg9 (997 amino acids), Sec9 (651 amino acids), Sso1 (290 amino acids) and Sec22 (214 amino acids) were downloaded from the National Center for Biotechnology Information (NCBI) and converted into musical notes as described in Materials and Methods. After the musical scores were generated (see Fig. 1 for an example of partial musical scores, and see Figs. S1–S4 for the complete scores corresponding to each protein), we assigned a unique instrument to each musical output. A variety of instruments were assigned to each protein, and the optimal sound was determined based on the auditory clarity and uniqueness of each protein melody when multiple scores were combined. Atg9 is introduced first with marimba, Sso1 as flute, Sec9 as shamisen, and finally Sec22 as harp. The individual proteins can be heard in Supplemental Sound Tracks S1–4.

Figure 1. Musical scores for proteins presented in SNARE Dance. The first two stanzas of the scores for each of the four proteins represented in the musical composition are shown. The scores were generated as described in Materials and Methods.

Orchestration

After assigning instruments to each protein score, we proceeded to combine the individual scores into a final orchestration; the arrangement was based on the biological interactions of each protein. We decided to begin with Atg9, which is the critical component of our piece involved in phagophore and autophagosome formation. Next, we introduced Sso1, followed by Sec9 and finally Sec22. The partial overlap of the music represents the SNARE-pairing. In the end, Atg9 reappears, which is meant to signify the self-interaction of this protein, which is important in Atg9 function.⁸ The final orchestration can be heard in Sound Track 1. (www.landesbioscience.com/journals/autophagy/article/19327)

Discussion

For more than three decades, researchers have attempted to use sound to assist in data presentation.^9-11 In part, sound is preferred because it can be perceived in a more quantitative manner than most human senses.¹⁰ Several parameters of sound can be used to provide information, including pitch, loudness, direction, duration/repetition and pause.¹⁰ Studies suggest that auditory data presentations are superior to visual, or even audiovisual, ones for discriminating among protein structural alignment parameters.¹² Accordingly, “sonification” (the rendition of data into sounds)¹³ or “audification” (using the sense of hearing to analyze data)¹⁴ provide useful avenues to enhance our ability to appreciate and understand complex biological processes.

The SNARE Dance is one example of the musical interpretation of a biological process, and it illustrates one step of macroautophagy, movement of Atg9 to the TVC in a manner that is dependent on the SNARE proteins Sso1, Sec9 and Sec22. Clearly other parts of autophagy can also be depicted in this manner, and additional proteins can be portrayed. We specifically omitted Atg11, Atg23 and Atg27 from the SNARE Dance because these proteins appear to affect Atg9 movement from the TVC to the PAS,^3,15 a step that occurs after the one being depicted here. Moreover, in SNARE Dance, we aimed to focus on individual sounds representing each protein in this musical conversion to portray the molecular-level interactions as opposed to large-scale cellular processes where the listener may lose the individual melodies associated with each protein. A future direction includes the incorporation of all proteins involved in a single step of macroautophagy or multiple steps involving multiple proteins. Such a musical output would most likely require that we group proteins based on sequence homology or function using a full orchestration that includes multiple instrument families (horns, woodwinds, strings, percussion, etc.). The output would allow the researcher/artist to depict and hear the united sound of a multilayered process rather than the molecular level interactions that we have displayed here. We hope that SNARE Dance has proven to be intriguing, and has added a new dimension to the appreciation of the dynamic process of autophagy.

Materials and Methods

Protein-coding sequences of Atg9 (NM_001180209.1), Sso1 (NM_001184046.1), Sec9 (NM_001181138.1) and Sec22 (NM_001182155.1) were converted to music as previously described.¹ Protein sequences were obtained from NCBI, converted to musical notes using the Gene2Music algorithm, and visualized using Finale Music Notation Software (MakeMusic Inc., Eden Prairie). The framework and order of proteins was drafted by Daniel J. Klionsky and the musical composition was created by Rie Takahashi. The conversion and creation of the final piece was prepared in multiple steps. First, each protein sequence was converted to music using piano as a common instrument in order to standardize the sound of each protein and identify distinct protein patterns and signatures. Second, based on the note range, length and overall texture of each protein, various instruments were assigned to each protein so that the listener would be able to recognize the individual proteins when played simultaneously. A number of instrumental combinations were derived that included, for example, only strings, or strings and woodwinds. The final orchestration represented the string, woodwind and percussion families. Specifically, Atg9 was played by marimba, Sso1 by flute, Sec9 by shamisen, and Sec22 by harp. The four representative instruments were then merged to produce an orchestration. The proteins were introduced in the following order: Atg9, Sso1, Sec9 and Sec22. Scientific properties such as protein-protein interactions were taken into consideration when merging the protein scores, and overlapping instruments in the music represent such properties.