1
|
Yang L, Yang Y, Liu X, Chen Y, Chen Y, Lin Y, Sun Y, Shen B. CHDGKB: a knowledgebase for systematic understanding of genetic variations associated with non-syndromic congenital heart disease. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021; 2020:5865522. [PMID: 32608479 PMCID: PMC7327432 DOI: 10.1093/database/baaa048] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 05/18/2020] [Accepted: 05/27/2020] [Indexed: 02/07/2023]
Abstract
Congenital heart disease (CHD) is one of the most common birth defects, with complex genetic and environmental etiologies. The reports of genetic variation associated with CHD have increased dramatically in recent years due to the revolutionary development of molecular technology. However, CHD is a heterogeneous disease, and its genetic origins remain inconclusive in most patients. Here we present a database of genetic variations for non-syndromic CHD (NS-CHD). By manually literature extraction and analyses, 5345 NS-CHD-associated genetic variations were collected, curated and stored in the public online database. The objective of our database is to provide the most comprehensive updates on NS-CHD genetic research and to aid systematic analyses of pathogenesis of NS-CHD in molecular level and the correlation between NS-CHD genotypes and phenotypes. Database URL: http://www.sysbio.org.cn/CHDGKB/.
Collapse
Affiliation(s)
- Lan Yang
- Center for Systems Biology, Soochow University, Suzhou 215006, China.,Center of Prenatal Diagnosis, Wuxi Maternal and Child Health Hospital Affiliated to Nanjing Medical University, Wuxi 214002, China
| | - Yang Yang
- School of Computer Science and Technology, Soochow University, Suzhou 215006, China
| | - Xingyun Liu
- Center for Systems Biology, Soochow University, Suzhou 215006, China.,Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yongquan Chen
- School of Computer Science and Technology, Soochow University, Suzhou 215006, China
| | - Yalan Chen
- Center for Systems Biology, Soochow University, Suzhou 215006, China
| | - Yuxin Lin
- Center for Systems Biology, Soochow University, Suzhou 215006, China
| | - Yan Sun
- Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Bairong Shen
- Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu 610041, China
| |
Collapse
|
2
|
Russell B, Solís C. Mechanosignaling pathways alter muscle structure and function by post-translational modification of existing sarcomeric proteins to optimize energy usage. J Muscle Res Cell Motil 2021; 42:367-380. [PMID: 33595762 DOI: 10.1007/s10974-021-09596-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 01/04/2021] [Indexed: 12/29/2022]
Abstract
A transduced mechanical signal arriving at its destination in muscle alters sarcomeric structure and function. A major question addressed is how muscle mass and tension generation are optimized to match actual performance demands so that little energy is wasted. Three cases for improved energy efficiency are examined: the troponin complex for tuning force production, control of the myosin heads in a resting state, and the Z-disc proteins for sarcomere assembly. On arrival, the regulation of protein complexes is often controlled by post-translational modification (PTM), of which the most common are phosphorylation by kinases, deacetylation by histone deacetylases and ubiquitination by E3 ligases. Another branch of signals acts not through peptide covalent bonding but via ligand interactions (e.g. Ca2+ and phosphoinositide binding). The myosin head and the regulation of its binding to actin by the troponin complex is the best and earliest example of signal destinations that modify myofibrillar contractility. PTMs in the troponin complex regulate both the efficiency of the contractile function to match physiologic demand for work, and muscle mass via protein degradation. The regulation of sarcomere assembly by integration of incoming signaling pathways causing the same PTMs or ligand binding are discussed in response to mechanical loading and unloading by the Z-disc proteins CapZ, α-actinin, telethonin, titin N-termini, and others. Many human mutations that lead to cardiomyopathy and heart disease occur in the proteins discussed above, which often occur at their PTM or ligand binding sites.
Collapse
Affiliation(s)
- Brenda Russell
- Department of Physiology and Biophysics, College of Medicine, University of Illinois at Chicago, Chicago, IL, 60612, USA.
| | - Christopher Solís
- Department of Physiology and Biophysics, College of Medicine, University of Illinois at Chicago, Chicago, IL, 60612, USA
| |
Collapse
|
3
|
Karam CN, Warren CM, Henze M, Banke NH, Lewandowski ED, Solaro RJ. Peroxisome proliferator-activated receptor-α expression induces alterations in cardiac myofilaments in a pressure-overload model of hypertrophy. Am J Physiol Heart Circ Physiol 2017; 312:H681-H690. [PMID: 28130336 DOI: 10.1152/ajpheart.00469.2016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 01/04/2017] [Accepted: 01/17/2017] [Indexed: 01/22/2023]
Abstract
Although alterations in fatty acid (FA) metabolism have been shown to have a negative impact on contractility of the hypertrophied heart, the targets of action remain elusive. In this study we compared the function of skinned fiber bundles from transgenic (Tg) mice that overexpress a relatively low level of the peroxisome proliferator-activated receptor α (PPARα), and nontransgenic (NTg) littermates. The mice (NTg-T and Tg-T) were stressed by transverse aortic constriction (TAC) and compared with shams (NTg-S and Tg-S). There was an approximate 4-fold increase in PPARα expression in Tg-S compared with NTg-S, but Tg-T hearts showed the same PPARα expression as NTg-T. Expression of PPARα did not alter the hypertrophic response to TAC but did reduce ejection fraction (EF) in Tg-T hearts compared with other groups. The rate of actomyosin ATP hydrolysis was significantly higher in Tg-S skinned fiber bundles compared with all other groups. Tg-T hearts showed an increase in phosphorylation of specific sites on cardiac myosin binding protein-C (cMyBP-C) and β-myosin heavy chain isoform. These results advance our understanding of potential signaling to the myofilaments induced by altered FA metabolism under normal and pathological states. We demonstrate that chronic and transient PPARα activation during pathological stress alters myofilament response to Ca2+ through a mechanism that is possibly mediated by MyBP-C phosphorylation and myosin heavy chain isoforms.NEW & NOTEWORTHY Data presented here demonstrate novel signaling to sarcomeric proteins by chronic alterations in fatty acid metabolism induced by PPARα. The mechanism involves modifications of key myofilament regulatory proteins modifying cross-bridge dynamics with differential effects in controls and hearts stressed by pressure overload.
Collapse
Affiliation(s)
- Chehade N Karam
- Department of Physiology & Biophysics, Center for Cardiovascular Research, University of Illinois at Chicago, Chicago, Illinois; and
| | - Chad M Warren
- Department of Physiology & Biophysics, Center for Cardiovascular Research, University of Illinois at Chicago, Chicago, Illinois; and
| | - Marcus Henze
- Department of Physiology & Biophysics, Center for Cardiovascular Research, University of Illinois at Chicago, Chicago, Illinois; and
| | - Natasha H Banke
- Department of Physiology & Biophysics, Center for Cardiovascular Research, University of Illinois at Chicago, Chicago, Illinois; and
| | - E Douglas Lewandowski
- Department of Physiology & Biophysics, Center for Cardiovascular Research, University of Illinois at Chicago, Chicago, Illinois; and.,Sanford Burnham Presbyterian Medical Discovery Institute, Orlando, Florida
| | - R John Solaro
- Department of Physiology & Biophysics, Center for Cardiovascular Research, University of Illinois at Chicago, Chicago, Illinois; and
| |
Collapse
|
4
|
Cheng Y, Regnier M. Cardiac troponin structure-function and the influence of hypertrophic cardiomyopathy associated mutations on modulation of contractility. Arch Biochem Biophys 2016; 601:11-21. [PMID: 26851561 PMCID: PMC4899195 DOI: 10.1016/j.abb.2016.02.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Revised: 01/30/2016] [Accepted: 02/02/2016] [Indexed: 11/29/2022]
Abstract
Cardiac troponin (cTn) acts as a pivotal regulator of muscle contraction and relaxation and is composed of three distinct subunits (cTnC: a highly conserved Ca(2+) binding subunit, cTnI: an actomyosin ATPase inhibitory subunit, and cTnT: a tropomyosin binding subunit). In this mini-review, we briefly summarize the structure-function relationship of cTn and its subunits, its modulation by PKA-mediated phosphorylation of cTnI, and what is known about how these properties are altered by hypertrophic cardiomyopathy (HCM) associated mutations of cTnI. This includes recent work using computational modeling approaches to understand the atomic-based structural level basis of disease-associated mutations. We propose a viewpoint that it is alteration of cTnC-cTnI interaction (rather than the Ca(2+) binding properties of cTn) per se that disrupt the ability of PKA-mediated phosphorylation at cTnI Ser-23/24 to alter contraction and relaxation in at least some HCM-associated mutations. The combination of state of the art biophysical approaches can provide new insight on the structure-function mechanisms of contractile dysfunction resulting cTnI mutations and exciting new avenues for the diagnosis, prevention, and even treatment of heart diseases.
Collapse
Affiliation(s)
- Yuanhua Cheng
- University of Washington, Department of Bioengineering, Seattle, WA, USA
| | - Michael Regnier
- University of Washington, Department of Bioengineering, Seattle, WA, USA.
| |
Collapse
|
5
|
Scruggs SB, Wang D, Ping P. PRKCE gene encoding protein kinase C-epsilon-Dual roles at sarcomeres and mitochondria in cardiomyocytes. Gene 2016; 590:90-6. [PMID: 27312950 DOI: 10.1016/j.gene.2016.06.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 05/23/2016] [Accepted: 06/05/2016] [Indexed: 12/26/2022]
Abstract
Protein kinase C-epsilon (PKCε) is an isoform of a large PKC family of enzymes that has a variety of functions in different cell types. Here we discuss two major roles of PKCε in cardiac muscle cells; specifically, its role in regulating cardiac muscle contraction via targeting the sarcomeric proteins, as well as modulating cardiac cell energy production and metabolism by targeting cardiac mitochondria. The importance of PKCε action is described within the context of intracellular localization, as substrate selectivity and specificity is achieved through spatiotemporal targeting of PKCε. Accordingly, the role of PKCε in regulating myocardial function in physiological and pathological states has been documented in both cardioprotection and cardiac hypertrophy.
Collapse
Affiliation(s)
- Sarah B Scruggs
- Departments of Physiology, Medicine (Cardiology) and Bioinformatics, NIH BD2K Center of Excellence for Biomedical Computing, University of California Los Angeles, Los Angeles, CA 90095, USA.
| | - Ding Wang
- Departments of Physiology, Medicine (Cardiology) and Bioinformatics, NIH BD2K Center of Excellence for Biomedical Computing, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Peipei Ping
- Departments of Physiology, Medicine (Cardiology) and Bioinformatics, NIH BD2K Center of Excellence for Biomedical Computing, University of California Los Angeles, Los Angeles, CA 90095, USA.
| |
Collapse
|
6
|
Trenchevska O, Nelson RW, Nedelkov D. Mass Spectrometric Immunoassays in Characterization of Clinically Significant Proteoforms. Proteomes 2016; 4:proteomes4010013. [PMID: 28248223 PMCID: PMC5217360 DOI: 10.3390/proteomes4010013] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 03/10/2016] [Accepted: 03/14/2016] [Indexed: 02/07/2023] Open
Abstract
Proteins can exist as multiple proteoforms in vivo, as a result of alternative splicing and single-nucleotide polymorphisms (SNPs), as well as posttranslational processing. To address their clinical significance in a context of diagnostic information, proteoforms require a more in-depth analysis. Mass spectrometric immunoassays (MSIA) have been devised for studying structural diversity in human proteins. MSIA enables protein profiling in a simple and high-throughput manner, by combining the selectivity of targeted immunoassays, with the specificity of mass spectrometric detection. MSIA has been used for qualitative and quantitative analysis of single and multiple proteoforms, distinguishing between normal fluctuations and changes related to clinical conditions. This mini review offers an overview of the development and application of mass spectrometric immunoassays for clinical and population proteomics studies. Provided are examples of some recent developments, and also discussed are the trends and challenges in mass spectrometry-based immunoassays for the next-phase of clinical applications.
Collapse
Affiliation(s)
- Olgica Trenchevska
- The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA.
| | - Randall W Nelson
- The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA.
| | - Dobrin Nedelkov
- The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA.
| |
Collapse
|
7
|
Gunther LK, Feng HZ, Wei H, Raupp J, Jin JP, Sakamoto T. Effect of N-Terminal Extension of Cardiac Troponin I on the Ca(2+) Regulation of ATP Binding and ADP Dissociation of Myosin II in Native Cardiac Myofibrils. Biochemistry 2016; 55:1887-97. [PMID: 26862665 DOI: 10.1021/acs.biochem.5b01059] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cardiac troponin I (cTnI) has a unique N-terminal extension that plays a role in modifying the calcium regulation of cardiac muscle contraction. Restrictive cleavage of the N-terminal extension of cTnI occurs under stress conditions as a physiological adaptation. Recent studies have shown that in comparison with controls, transgenic mouse cardiac myofibrils containing cTnI lacking the N-terminal extension (cTnI-ND) had a lower sensitivity to calcium activation of ATPase, resulting in enhanced ventricular relaxation and cardiac function. To investigate which step(s) of the ATPase cycle is regulated by the N-terminal extension of cTnI, here we studied the calcium dependence of cardiac myosin II ATPase kinetics in isolated cardiac myofibrils. ATP binding and ADP dissociation rates were measured by using stopped-flow spectrofluorimetry with mant-dATP and mant-dADP, respectively. We found that the second-order mant-dATP binding rate of cTnI-ND mouse cardiac myofibrils was 3-fold faster than that of wild-type myofibrils at low Ca(2+) concentrations. The ADP dissociation rate of cTnI-ND myofibrils was positively dependent on calcium concentration, while the wild-type controls were not significantly affected. These data from experiments using native cardiac myofibrils under physiological conditions indicate that modification of the N-terminal extension of cTnI plays a role in the calcium regulation of the kinetics of actomyosin ATPase.
Collapse
Affiliation(s)
- Laura K Gunther
- Department of Physics and Astronomy, Wayne State University , Detroit, Michigan 48201, United States
| | - Han-Zhong Feng
- Department of Physiology, Wayne State University School of Medicine , Detroit, Michigan 48201, United States
| | - Hongguang Wei
- Department of Physiology, Wayne State University School of Medicine , Detroit, Michigan 48201, United States
| | - Justin Raupp
- Department of Physics and Astronomy, Wayne State University , Detroit, Michigan 48201, United States
| | - Jian-Ping Jin
- Department of Physiology, Wayne State University School of Medicine , Detroit, Michigan 48201, United States
| | - Takeshi Sakamoto
- Department of Physics and Astronomy, Wayne State University , Detroit, Michigan 48201, United States.,Department of Physiology, Wayne State University School of Medicine , Detroit, Michigan 48201, United States
| |
Collapse
|
8
|
Zhang M, Martin JL, Kumar M, Khairallah RJ, de Tombe PP. Rapid large-scale purification of myofilament proteins using a cleavable His6-tag. Am J Physiol Heart Circ Physiol 2015; 309:H1509-15. [PMID: 26386113 PMCID: PMC4666967 DOI: 10.1152/ajpheart.00598.2015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 09/15/2015] [Indexed: 11/22/2022]
Abstract
With the advent of high-throughput DNA sequencing, the number of identified cardiomyopathy-causing mutations has increased tremendously. As the majority of these mutations affect myofilament proteins, there is a need to understand their functional consequence on contraction. Permeabilized myofilament preparations coupled with protein exchange protocols are a common method for examining into contractile mechanics. However, producing large quantities of myofilament proteins can be time consuming and requires different approaches for each protein of interest. In the present study, we describe a unified automated method to produce troponin C, troponin T, and troponin I as well as myosin light chain 2 fused to a His6-tag followed by a tobacco etch virus (TEV) protease site. TEV protease has the advantage of a relaxed P1' cleavage site specificity, allowing for no residues left after proteolysis and preservation of the native sequence of the protein of interest. After expression in Esherichia coli, cells were lysed by sonication in imidazole-containing buffer. The His6-tagged protein was then purified using a HisTrap nickel metal affinity column, and the His6-tag was removed by His6-TEV protease digestion for 4 h at 30°C. The protease was then removed using a HisTrap column, and complex assembly was performed via column-assisted sequential desalting. This mostly automated method allows for the purification of protein in 1 day and can be adapted to most soluble proteins. It has the advantage of greatly increasing yield while reducing the time and cost of purification. Therefore, production and purification of mutant proteins can be accelerated and functional data collected in a faster, less expensive manner.
Collapse
Affiliation(s)
- Mengjie Zhang
- Department of Cell and Molecular Physiology, Loyola University, Chicago, Illinois
| | - Jody L Martin
- Department of Cell and Molecular Physiology, Loyola University, Chicago, Illinois
| | - Mohit Kumar
- Department of Cell and Molecular Physiology, Loyola University, Chicago, Illinois
| | - Ramzi J Khairallah
- Department of Cell and Molecular Physiology, Loyola University, Chicago, Illinois
| | - Pieter P de Tombe
- Department of Cell and Molecular Physiology, Loyola University, Chicago, Illinois
| |
Collapse
|
9
|
The cardiac-specific N-terminal region of troponin I positions the regulatory domain of troponin C. Proc Natl Acad Sci U S A 2014; 111:14412-7. [PMID: 25246568 DOI: 10.1073/pnas.1410775111] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The cardiac isoform of troponin I (cTnI) has a unique 31-residue N-terminal region that binds cardiac troponin C (cTnC) to increase the calcium sensitivity of the sarcomere. The interaction can be abolished by cTnI phosphorylation at Ser22 and Ser23, an important mechanism for regulating cardiac contractility. cTnC contains two EF-hand domains (the N and C domain of cTnC, cNTnC and cCTnC) connected by a flexible linker. Calcium binding to either domain favors an "open" conformation, exposing a large hydrophobic surface that is stabilized by target binding, cTnI[148-158] for cNTnC and cTnI[39-60] for cCTnC. We used multinuclear multidimensional solution NMR spectroscopy to study cTnI[1-73] in complex with cTnC. cTnI[39-60] binds to the hydrophobic face of cCTnC, stabilizing an alpha helix in cTnI[41-67] and a type VIII turn in cTnI[38-41]. In contrast, cTnI[1-37] remains disordered, although cTnI[19-37] is electrostatically tethered to the negatively charged surface of cNTnC (opposite its hydrophobic surface). The interaction does not directly affect the calcium binding affinity of cNTnC. However, it does fix the positioning of cNTnC relative to the rest of the troponin complex, similar to what was previously observed in an X-ray structure [Takeda S, et al. (2003) Nature 424(6944):35-41]. Domain positioning impacts the effective concentration of cTnI[148-158] presented to cNTnC, and this is how cTnI[19-37] indirectly modulates the calcium affinity of cNTnC within the context of the cardiac thin filament. Phosphorylation of cTnI at Ser22/23 disrupts domain positioning, explaining how it impacts many other cardiac regulatory mechanisms, like the Frank-Starling law of the heart.
Collapse
|
10
|
Abstract
We focus here on the modulation of thin filament activity by cardiac troponin I phosphorylation as an integral and adaptive mechanism in cardiac homeostasis and as a mechanism vulnerable to maladaptive response to stress. We discuss a current concept of cardiac troponin I function in the A-band region of the sarcomere and potential signaling to cardiac troponin I in a network involving the ends of the thin filaments at the Z-disk and the M-band regions. The cardiac sarcomere represents a remarkable set of interacting proteins that functions not only as a molecular machine generating the heartbeat but also as a hub of signaling. We review how phosphorylation signaling to cardiac troponin I is integrated, with parallel signals controlling excitation-contraction coupling, hypertrophy, and metabolism.
Collapse
Affiliation(s)
- R John Solaro
- Department of Physiology and Biophysics and Center for Cardiovascular Research, University of Illinois at Chicago, College of Medicine, Chicago, IL 60612, USA.
| | | | | |
Collapse
|