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Yaoita H, Kawai E, Takayama J, Iwasawa S, Saijo N, Abiko M, Suzuki K, Kimura M, Ozawa A, Tamiya G, Kure S, Kikuchi A. Genetic etiology of truncus arteriosus excluding 22q11.2 deletion syndrome and identification of c.1617del, a prevalent variant in TMEM260, in the Japanese population. J Hum Genet 2024; 69:177-183. [PMID: 38351237 PMCID: PMC11043042 DOI: 10.1038/s10038-024-01223-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/05/2024] [Accepted: 01/25/2024] [Indexed: 02/19/2024]
Abstract
Truncus Arteriosus (TA) is a congenital heart disease characterized by a single common blood vessel emerging from the right and left ventricles instead of the main pulmonary artery and aorta. TA accounts for 4% of all critical congenital heart diseases. The most common cause of TA is 22q11.2 deletion syndrome, accounting for 12-35% of all TA cases. However, no major causes of TA other than 22q11.2 deletion have been reported. We performed whole-genome sequencing of 11 Japanese patients having TA without 22q11.2 deletion. Among five patients, we identified pathogenic variants in TMEM260; the biallelic loss-of-function variants of which have recently been associated with structural heart defects and renal anomalies syndrome (SHDRA). In one patient, we identified a de novo pathogenic variant in GATA6, and in another patient, we identified a de novo probably pathogenic variant in NOTCH1. Notably, we identified a prevalent variant in TMEM260 (ENST00000261556.6), c.1617del (p.Trp539Cysfs*9), in 8/22 alleles among the 11 patients. The c.1617del variant was estimated to occur approximately 23 kiloyears ago. Based on the allele frequency of the c.1617del variant in the Japanese population (0.36%), approximately 26% of Japanese patients afflicted with TA could harbor homozygous c.1617del variants. This study highlights TMEM260, especially c.1617del, as a major genetic cause of TA in the Japanese population.
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Affiliation(s)
- Hisao Yaoita
- Department of Pediatrics, Tohoku University Graduate School of Medicine, Sendai, Japan.
| | - Eiichiro Kawai
- Department of Pediatric Cardiology, Miyagi Children's Hospital, Sendai, Japan
| | - Jun Takayama
- Department of AI and Innovative Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
- Tohoku Medical Megabank organization, Tohoku University, Sendai, Japan
- Statistical Genetics Team, RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
- Department of Rare Disease Genomics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Shinya Iwasawa
- Department of Pediatrics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Naoya Saijo
- Department of Pediatrics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Masayuki Abiko
- Department of Pediatrics, Yamagata University Graduate School of Medicine, Yamagata, Japan
| | - Kouta Suzuki
- Department of Pediatrics, Yamagata University Graduate School of Medicine, Yamagata, Japan
| | - Masato Kimura
- Department of Pediatric Cardiology, Miyagi Children's Hospital, Sendai, Japan
| | - Akira Ozawa
- Department of Pediatric Cardiology, Miyagi Children's Hospital, Sendai, Japan
| | - Gen Tamiya
- Department of AI and Innovative Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
- Tohoku Medical Megabank organization, Tohoku University, Sendai, Japan
- Statistical Genetics Team, RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
- Department of Rare Disease Genomics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Shigeo Kure
- Department of Pediatrics, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Rare Disease Genomics, Tohoku University Graduate School of Medicine, Sendai, Japan
- Miyagi Children's Hospital, Sendai, Japan
| | - Atsuo Kikuchi
- Department of Pediatrics, Tohoku University Graduate School of Medicine, Sendai, Japan.
- Department of Rare Disease Genomics, Tohoku University Graduate School of Medicine, Sendai, Japan.
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Inoue T, Takase R, Uchida K, Kodo K, Suda K, Watanabe Y, Yoshiura KI, Kunimatsu M, Ishizaki R, Azuma K, Inai K, Muneuchi J, Furutani Y, Akagawa H, Yamagishi H. The c.1617del variant of TMEM260 is identified as the most frequent single gene determinant for Japanese patients with a specific type of congenital heart disease. J Hum Genet 2024; 69:215-222. [PMID: 38409496 PMCID: PMC11043032 DOI: 10.1038/s10038-024-01225-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 01/15/2024] [Accepted: 01/26/2024] [Indexed: 02/28/2024]
Abstract
Although the molecular mechanisms underlying congenital heart disease (CHD) remain poorly understood, recent advances in genetic analysis have facilitated the exploration of causative genes for CHD. We reported that the pathogenic variant c.1617del of TMEM260, which encodes a transmembrane protein, is highly associated with CHD, specifically persistent truncus arteriosus (PTA), the most severe cardiac outflow tract (OFT) defect. Using whole-exome sequencing, the c.1617del variant was identified in two siblings with PTA in a Japanese family and in three of the 26 DNAs obtained from Japanese individuals with PTA. The c.1617del of TMEM260 has been found only in East Asians, especially Japanese and Korean populations, and the frequency of this variant in PTA is estimated to be next to that of the 22q11.2 deletion, the most well-known genetic cause of PTA. Phenotype of patients with c.1617del appears to be predominantly in the heart, although TMEM260 is responsible for structural heart defects and renal anomalies syndrome (SHDRA). The mouse TMEM260 variant (p.W535Cfs*56), synonymous with the human variant (p.W539Cfs*9), exhibited truncation and downregulation by western blotting, and aggregation by immunocytochemistry. In situ hybridization demonstrated that Tmem260 is expressed ubiquitously during embryogenesis, including in the development of cardiac OFT implicated in PTA. This expression may be regulated by a ~ 0.8 kb genomic region in intron 3 of Tmem260 that includes multiple highly conserved binding sites for essential cardiac transcription factors, thus revealing that the c.1617del variant of TMEM260 is the major single-gene variant responsible for PTA in the Japanese population.
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Affiliation(s)
- Tadashi Inoue
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
- Department of Pediatrics and Child Health, Kurume University School of Medicine, Fukuoka, Japan
| | - Ryuta Takase
- Department of Pediatrics and Child Health, Kurume University School of Medicine, Fukuoka, Japan
| | - Keiko Uchida
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan.
- Keio University Health Center, Tokyo, Japan.
| | - Kazuki Kodo
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Kenji Suda
- Department of Pediatrics and Child Health, Kurume University School of Medicine, Fukuoka, Japan
| | - Yoriko Watanabe
- Department of Pediatrics and Child Health, Kurume University School of Medicine, Fukuoka, Japan
- Research Institute of Medical Mass Spectrometry, Kurume University School of Medicine, Fukuoka, Japan
| | - Koh-Ichiro Yoshiura
- Department of Human Genetics, Division of Advanced Preventive Medical Sciences, Leading Medical Research Core Unit, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Masaya Kunimatsu
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
- Department of Pediatrics, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Reina Ishizaki
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Kenko Azuma
- Institute for Comprehensive Medical Sciences, Tokyo Women's Medical University, Tokyo, Japan
| | - Kei Inai
- Department of Pediatric Cardiology and Adult Congenital Cardiology, Tokyo Women's Medical University, Tokyo, Japan
| | - Jun Muneuchi
- Department of Pediatrics, Kyushu Hospital, Japan Community Healthcare Organization, Kitakyushu, Japan
| | - Yoshiyuki Furutani
- Department of Pediatric Cardiology and Adult Congenital Cardiology, Tokyo Women's Medical University, Tokyo, Japan
| | - Hiroyuki Akagawa
- Institute for Comprehensive Medical Sciences, Tokyo Women's Medical University, Tokyo, Japan
| | - Hiroyuki Yamagishi
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
- Center for Preventive Medicine, Keio University School of Medicine, Tokyo, Japan
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Bains RK, Nasseri SA, Wardman JF, Withers SG. Advances in the understanding and exploitation of carbohydrate-active enzymes. Curr Opin Chem Biol 2024; 80:102457. [PMID: 38657391 DOI: 10.1016/j.cbpa.2024.102457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/29/2024] [Accepted: 04/01/2024] [Indexed: 04/26/2024]
Abstract
Carbohydrate-active enzymes (CAZymes) are responsible for the biosynthesis, modification and degradation of all glycans in Nature. Advances in genomic and metagenomic methodologies, in conjunction with lower cost gene synthesis, have provided access to a steady stream of new CAZymes with both well-established and novel mechanisms. At the same time, increasing access to cryo-EM has resulted in exciting new structures, particularly of transmembrane glycosyltransferases of various sorts. This improved understanding has resulted in widespread progress in applications of CAZymes across diverse fields, including therapeutics, organ transplantation, foods, and biofuels. Herein, we highlight a few of the many important advances that have recently been made in the understanding and applications of CAZymes.
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Affiliation(s)
- Rajneesh K Bains
- Department of Chemistry, University of British Columbia, Vancouver, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
| | - Seyed Amirhossein Nasseri
- Department of Chemistry, University of British Columbia, Vancouver, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
| | - Jacob F Wardman
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada; Department of Biochemistry, University of British Columbia, Vancouver, Canada
| | - Stephen G Withers
- Department of Chemistry, University of British Columbia, Vancouver, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, Canada; Department of Biochemistry, University of British Columbia, Vancouver, Canada.
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Sanji AS, J M, Gurav MJ, Batra SK, Chachadi VB. Cancer snap-shots: Biochemistry and glycopathology of O-glycans: A review. Int J Biol Macromol 2024; 260:129318. [PMID: 38232866 DOI: 10.1016/j.ijbiomac.2024.129318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/05/2024] [Accepted: 01/05/2024] [Indexed: 01/19/2024]
Abstract
Cancer pathogenesis is strongly linked to the qualitative and quantitative alteration of the cell surface glycans, that are glycosidically linked to proteins and lipids. Glycans that are covalently linked to the polypeptide backbone of a protein through nitrogen or oxygen, are known as N-glycans or O-glycans, respectively. Although the role of glycans in the expression, physiology, and communication of cells is well documented, the function of these glycans in tumor biology is not fully elucidated. In this context, current review summarizes biosynthesis, modifications and pathological implications of O-glycans The review also highlights illustrative examples of cancer types modulated by aberrant O-glycosylation. Related O-glycans like Thomsen-nouveau (Tn), Thomsen-Friedenreich (TF), Lewisa/x, Lewisb/y, sialyl Lewisa/x and some other O-glycans are discussed in detail. Since, the overexpression of O-glycans are attributed to the aggressiveness and metastatic behavior of cancer cells, the current review attempts to understand the relation between metastasis and O-glycans.
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Affiliation(s)
- Ashwini S Sanji
- P. G. Department of Studies in Biochemistry, Karnatak University, Dharwad, Karnataka 580 003, India
| | - Manasa J
- P. G. Department of Studies in Biochemistry, Karnatak University, Dharwad, Karnataka 580 003, India
| | - Maruti J Gurav
- P. G. Department of Studies in Biochemistry, Karnatak University, Dharwad, Karnataka 580 003, India
| | - Surinder K Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA; Fred and Pamela Buffett Cancer Center, Eppley Institute for Research in Cancer and Allied Disease, University of Nebraska Medical Center, Omaha, NE, USA
| | - Vishwanath B Chachadi
- P. G. Department of Studies in Biochemistry, Karnatak University, Dharwad, Karnataka 580 003, India.
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Poulhazan A, Arnold AA, Mentink-Vigier F, Muszyński A, Azadi P, Halim A, Vakhrushev SY, Joshi HJ, Wang T, Warschawski DE, Marcotte I. Molecular-level architecture of Chlamydomonas reinhardtii's glycoprotein-rich cell wall. Nat Commun 2024; 15:986. [PMID: 38307857 PMCID: PMC10837150 DOI: 10.1038/s41467-024-45246-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 01/19/2024] [Indexed: 02/04/2024] Open
Abstract
Microalgae are a renewable and promising biomass for large-scale biofuel, food and nutrient production. However, their efficient exploitation depends on our knowledge of the cell wall composition and organization as it can limit access to high-value molecules. Here we provide an atomic-level model of the non-crystalline and water-insoluble glycoprotein-rich cell wall of Chlamydomonas reinhardtii. Using in situ solid-state and sensitivity-enhanced nuclear magnetic resonance, we reveal unprecedented details on the protein and carbohydrate composition and their nanoscale heterogeneity, as well as the presence of spatially segregated protein- and glycan-rich regions with different dynamics and hydration levels. We show that mannose-rich lower-molecular-weight proteins likely contribute to the cell wall cohesion by binding to high-molecular weight protein components, and that water provides plasticity to the cell-wall architecture. The structural insight exemplifies strategies used by nature to form cell walls devoid of cellulose or other glycan polymers.
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Affiliation(s)
- Alexandre Poulhazan
- Department of Chemistry, Université du Québec à Montréal, Montreal, QC, H2X 2J6, Canada
| | - Alexandre A Arnold
- Department of Chemistry, Université du Québec à Montréal, Montreal, QC, H2X 2J6, Canada
| | - Frederic Mentink-Vigier
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL, 32310, USA
| | - Artur Muszyński
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Adnan Halim
- Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark
| | | | - Tuo Wang
- Department of Chemistry, Michigan State University, East Lansing, MI, 48824, USA.
| | - Dror E Warschawski
- Laboratoire des Biomolécules, LBM, CNRS UMR 7203, Sorbonne Université, École Normale Supérieure, PSL University, 75005, Paris, France.
| | - Isabelle Marcotte
- Department of Chemistry, Université du Québec à Montréal, Montreal, QC, H2X 2J6, Canada.
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Géraud N, Falcou C, Parra J, Froment C, Rengel D, Burlet-Schiltz O, Marcoux J, Nigou J, Rivière M, Fabre E. Development of a novel target-based cell assay, reporter of the activity of Mycobacterium tuberculosis protein-O-mannosyltransferase. Glycobiology 2023; 33:1139-1154. [PMID: 37698262 DOI: 10.1093/glycob/cwad072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/13/2023] Open
Abstract
The Protein-O-mannosyltransferase is crucial for the virulence of Mycobacterium tuberculosis, the etiological agent of tuberculosis. This enzyme, called MtPMT (Rv1002c), is responsible for the post-translational O-mannosylation of mycobacterial proteins. It catalyzes the transfer of a single mannose residue from a polyprenol phospho-mannosyl lipidic donor to the hydroxyl groups of selected Ser/Thr residues in acceptor proteins during their translocation across the membrane. Previously, we provided evidence that the loss of MtPMT activity causes the absence of mannoproteins in Mycobacterium tuberculosis, severely impacting its intracellular growth, as well as a strong attenuation of its pathogenicity in immunocompromised mice. Therefore, it is of interest to develop specific inhibitors of this enzyme to better understand mycobacterial infectious diseases. Here we report the development of a "target-based" phenotypic assay for this enzyme, assessing its O-mannosyltransferase activity in bacteria, in the non-pathogenic Mycobacterium smegmatis strain. Robustness of the quantitative contribution of this assay was evaluated by intact protein mass spectrometry, using a panel of control strains, overexpressing the MtPMT gene, carrying different key point-mutations. Then, screening of a limited library of 30 compounds rationally chosen allowed us to identify 2 compounds containing pyrrole analogous rings, as significant inhibitors of MtPMT activity, affecting neither the growth of the mycobacterium nor its secretion of mannoproteins. These molecular cores could therefore serve as scaffold for the design of new pharmaceutical agents that could improve treatment of mycobacterial diseases. We report here the implementation of a miniaturized phenotypic activity assay for a glycosyltransferase of the C superfamily.
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Affiliation(s)
- Nicolas Géraud
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III-Paul Sabatier (UT3), 31400 Toulouse, France
| | - Camille Falcou
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III-Paul Sabatier (UT3), 31400 Toulouse, France
| | - Julien Parra
- Infrastructure nationale de protéomique, ProFI, 205 Rte de Narbonne, 31400 Toulouse, France
| | - Carine Froment
- Infrastructure nationale de protéomique, ProFI, 205 Rte de Narbonne, 31400 Toulouse, France
| | - David Rengel
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III-Paul Sabatier (UT3), 31400 Toulouse, France
| | - Odile Burlet-Schiltz
- Infrastructure nationale de protéomique, ProFI, 205 Rte de Narbonne, 31400 Toulouse, France
| | - Julien Marcoux
- Infrastructure nationale de protéomique, ProFI, 205 Rte de Narbonne, 31400 Toulouse, France
| | - Jérôme Nigou
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III-Paul Sabatier (UT3), 31400 Toulouse, France
| | - Michel Rivière
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III-Paul Sabatier (UT3), 31400 Toulouse, France
| | - Emeline Fabre
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III-Paul Sabatier (UT3), 31400 Toulouse, France
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Koff M, Monagas-Valentin P, Novikov B, Chandel I, Panin V. Protein O-mannosylation: one sugar, several pathways, many functions. Glycobiology 2023; 33:911-926. [PMID: 37565810 PMCID: PMC10859634 DOI: 10.1093/glycob/cwad067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 07/23/2023] [Accepted: 07/31/2023] [Indexed: 08/12/2023] Open
Abstract
Recent research has unveiled numerous important functions of protein glycosylation in development, homeostasis, and diseases. A type of glycosylation taking the center stage is protein O-mannosylation, a posttranslational modification conserved in a wide range of organisms, from yeast to humans. In animals, protein O-mannosylation plays a crucial role in the nervous system, whereas protein O-mannosylation defects cause severe neurological abnormalities and congenital muscular dystrophies. However, the molecular and cellular mechanisms underlying protein O-mannosylation functions and biosynthesis remain not well understood. This review outlines recent studies on protein O-mannosylation while focusing on the functions in the nervous system, summarizes the current knowledge about protein O-mannosylation biosynthesis, and discusses the pathologies associated with protein O-mannosylation defects. The evolutionary perspective revealed by studies in the Drosophila model system are also highlighted. Finally, the review touches upon important knowledge gaps in the field and discusses critical questions for future research on the molecular and cellular mechanisms associated with protein O-mannosylation functions.
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Affiliation(s)
- Melissa Koff
- Department of Biochemistry and Biophysics, AgriLife Research, Texas A&M University, College Station, College Station, TX 77843, United States
| | - Pedro Monagas-Valentin
- Department of Biochemistry and Biophysics, AgriLife Research, Texas A&M University, College Station, College Station, TX 77843, United States
| | - Boris Novikov
- Department of Biochemistry and Biophysics, AgriLife Research, Texas A&M University, College Station, College Station, TX 77843, United States
| | - Ishita Chandel
- Department of Biochemistry and Biophysics, AgriLife Research, Texas A&M University, College Station, College Station, TX 77843, United States
| | - Vladislav Panin
- Department of Biochemistry and Biophysics, AgriLife Research, Texas A&M University, College Station, College Station, TX 77843, United States
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