盲鰻為脊椎動物最原始的姊妹群，屬於腐食動物，生活圈可達數千公尺水深。盲鰻的代謝速率及心臟效能是脊椎動物中表現最低的，本論文由蛋白體及代謝體層次去探討盲鰻特化的咬肌、低代謝速率的心肌和深海環境對其心肌的影響所展現的生化特徵。第一章及第二章發現creatine kinase在盲鰻體側肌及深海盲鰻心肌有大量表現，推測此酵素在深海動物體側肌及心肌在利用儲存的phosphocreatine扮演重要的角色。而在盲鰻咬肌和深海盲鰻心肌發現glycogen phosphorylase的大量表現，推測此二類的肌肉均進行無氧醣解作用。與海鱺和鮪魚比較，TMAO和尿素在盲鰻心肌含量較高，推測兩者功能在盲鰻心肌扮演維持滲透壓的物質，然而，TMAO而非尿素在深海盲鰻心肌卻含量較高，推測 TMAO不僅為維持滲透壓的功能，應有深度影響的相關生理有其相關性。 此外，nebulin在盲鰻心肌大量表現，而tropomyosin則在海鱺及鮪魚心肌大量表現，顯示他們的收縮特性的差異可能來自於蛋白質間的機制。本論文提供了盲鰻骨骼肌和心肌在生態生理適應上的可能候選蛋白質及代謝物。

Hagfish are the plesiomorphic sister group of all vertebrates. They are scavengers and many live at depths reaching thousands of meters. In addition, hagfish show the lowest metabolic rate as well as cardiac performance in vertebrates. This dissertation evaluated the biochemical characterizations of hagfish skeletal muscles related to the feeding apparatus and hagfish cardiac muscle associated with cardiac performance and deep-sea effects at the proteomic and metabolomic levels. In Chapter one and two, I found creatine kinase over-expressed in hagfish somatic muscle and deep-sea hagfish cardiac muscle, I suppose that this enzyme was important for utilization of stored phosphocreatine in deep-sea animals’ somatic muscle and cardiac muscle. Over-expressed glycogen phosphorylase in hagfish dental and deep-sea hagfish cardiac muscle supposes these two types of muscles undergoing the anaerobic glycolysis. Compared to teleosts (cobia and tuna), TMAO and urea were higher in hagfish suggest their functions in hagfish cardiac muscle as osmolytes, however, higher TMAO but not urea in deep-sea hagfish, I suggest TMAO functions not only as an osmolyte but also physiological impacts in hagfish cardiac muscle for depth-related adaptations. I also found higher nebulin express in hagfish cardiac muscle and higher tropomyosin express in cobia and tuna cardiac muscles, thus their contractile differentiations were resulted from the protein-protein mechanism. This dissertation provides candidate proteins and metabolits involved in ecophysiological adaptation of hagfish skeletal and cardiac muscles.

ABSTRACT........................................................................................................ i
Figure List.......................................................................................................... x
Table List........................................................................................................... xii
INTRODUCTION.............................................................................................. 1
1 Differential proteome and metabolome expression of hagfish dental and somatic skeletal muscles
1.1 Summary.................................................................................................. 6
1.2 Introduction.............................................................................................. 7
1.3 Materials and Methods............................................................................. 10
1.3.1. Histochemistry................................................................................. 10
1.3.2. Extractions of proteins................................................................... 11
1.3.3. 2-DE run conditions....................................................................... 12
1.3.4. Image acquisition and data analysis............................................... 13
1.3.5. In-gel digestion and identification using MS................................... 14
1.3.6. Database search for MS data.......................................................... 15
1.3.7. Extraction of muscle metabolites................................................... 16
1.3.8. NMR spectroscopy........................................................................... 16
1.3.9. NMR data analysis........................................................................... 17
1.4 Results....................................................................................................... 18
1.4.1. Cross-sectional area of hagfish dental and somatic muscle fibers.. 18
1.4.2. 2-DE and reproducibility................................................................. 19
1.4.3. Differentially expressed spots between dental and somatic muscles.............................................................................................. 23
1.4.4. Protein isoforms............................................................................... 24
1.4.5. 1H NMR spectra............................................................................... 29
1.4.6. Pattern recognition........................................................................... 32
1.5 Discussion.................................................................................................. 35
1.5.1. Muscle metabolism.......................................................................... 35
1.5.2. Contractile proteins.......................................................................... 37
1.5.3. Protein isoforms............................................................................... 38
1.5.4. Implication of biochemical regulation in ecophysiology................. 40
1.5.5. Metabolomic differentiation............................................................. 43
1.6 Conclusion.................................................................................................. 46

2 Integration of proteomics and metabolomics for evaluation of depth-related effects on hagfish cardiac muscles
2.1 Summary.................................................................................................. 48
2.2 Introduction.............................................................................................. 49
2.3 Materials and Methods............................................................................. 51
2.3.1. Experimental subjects.................................................................... 51
2.3.2. Extraction of cardiac proteins and metabolite................................ 52
2.3.3. Gel electrophoresis run condition................................................... 52
2.3.4. MALDI-TOF MS(/MS) and database searching............................ 53
2.3.5. NMR spectroscopy......................................................................... 55
2.4 Results...................................................................................................... 55
2.4.1. 1DE and 2DE Protein patterns......................................................... 55
2.4.2. Identified proteins by MALDI TOF/TOF MS................................. 59
2.4.3. Pattern recognitions of 1H NMR spectra.......................................... 59
2.4.4. Assigned Metabolites....................................................................... 60
2.5 Discussion.................................................................................................. 60
2.5.1. Physiological function of creatine kinase in deep-sea organisms… 65

2.5.2. Biological Consequences of TMAO and urea in Hagfish Cardiac Muscles........................................................................................... 66
2.5.3. Phylogenetic effects? .................................................................... 68
2.6 Conclusion............................................................................................... 69
3 Biochemical characterizations of hagfish, cobia and tuna cardiac muscles
3.1 Summary.................................................................................................. 70
3.2 Introduction.............................................................................................. 71
3.3 Materials and Methods............................................................................. 73
3.3.1. Experimental subjects.................................................................... 73
3.3.2. Metabolomics approaches.............................................................. 74
3.3.3. Proteomics approaches................................................................... 74
3.4 Results...................................................................................................... 75
3.4.1. Descriptions of fish cardiac metabolites........................................ 75
3.4.2. Multivariate analyses of 1H NMR spectra..................................... 76
3.4.3. Protein patterns.............................................................................. 81
3.5 Discussion................................................................................................ 85
3.5.1. Osmolytes...................................................................................... 85
3.5.2. Energy metabolism....................................................................... 89
3.5.3. Myofibrilla proteins...................................................................... 92
3.6 Conclusion............................................................................................ 94
CONCLUSION................................................................................................. 95
REFERENCES.................................................................................................. 98
APPENDIX I: TABLES OF ABBREVIATIONS.......................................... 112
CURRICULUM VITAE.................................................................................... 113
REPRINT OF PUBLICATION FROM THE DISSERTATION.................... 114

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