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Case BF, Groffen J, Galligan TM, Bodinof Jachowski CM, Hallagan JJ, Hildreth SB, Alaasam V, Keith Ray W, Helm RF, Hopkins WA. Androgen and glucocorticoid profiles throughout extended uniparental paternal care in the eastern hellbender salamander (Cryptobranchus a. alleganiensis). Gen Comp Endocrinol 2024:114547. [PMID: 38772453 DOI: 10.1016/j.ygcen.2024.114547] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 05/08/2024] [Accepted: 05/15/2024] [Indexed: 05/23/2024]
Abstract
The behavioral endocrinology associated with reproduction and uniparental male care has been studied in teleosts, but little is known about hormonal correlates of uniparental male care in other ectotherms. To address this gap, we are the first to document the seasonal steroid endocrinology of uniparental male hellbender salamanders during the transition from pre-breeding to nest initiation, and through the subsequent eight months of paternal care. In doing so, we investigated the correlates of nest fate and clutch size, exploring hellbenders' alignment with several endocrinological patterns observed in uniparental male fish. Understanding the endocrinology of hellbender paternal care is also vital from a conservation perspective because high rates of nest failure were recently identified as a factor causing population declines in this imperiled species. We corroborated previous findings demonstrating testosterone and dihydrotestosterone (DHT) to be the primary androgens in hellbender reproduction, and that cortisol circulates as the most abundant glucocorticoid. However, we were unable to identify a prolactin or a "prolactin-like" peptide in circulation prior to or during parental care. We observed ∼ 80 % declines in both primary androgens during the transition from pre-breeding to nest initiation, and again as paternal care progressed past its first month. In the days immediately following nest initiation, testosterone and DHT trended higher in successful individuals, but did not differ with males' clutch size. We did not observe meaningful seasonality in baseline glucocorticoids associated with breeding or nesting. In contrast, stress-induced glucocorticoids were highest at pre-breeding and through the first two months of care, before declining during the latter-most periods of care as larvae approach emergence from the nest. Neither baseline nor stress-induced glucocorticoids varied significantly with either nest fate or clutch size. Both stress-induced cortisol and corticosterone were positively correlated with total length, a proxy for age in adult hellbenders. This is consistent with age-related patterns in some vertebrates, but the first such pattern observed in a wild amphibian population. Generally, we found that nesting hellbenders adhere to some but not all of the endocrinological patterns observed in uniparental male teleosts prior to and during parental care.
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Affiliation(s)
- Brian F Case
- Virginia Tech, Department of Fish and Wildlife Conservation, Blacksburg, VA 24060, USA.
| | - Jordy Groffen
- Virginia Tech, Department of Fish and Wildlife Conservation, Blacksburg, VA 24060, USA
| | - Thomas M Galligan
- Virginia Tech, Department of Fish and Wildlife Conservation, Blacksburg, VA 24060, USA
| | | | - John J Hallagan
- Virginia Tech, Department of Fish and Wildlife Conservation, Blacksburg, VA 24060, USA
| | - Sherry B Hildreth
- Virginia Tech, Fralin Life Sciences Institute, Blacksburg, VA 24060, USA
| | - Valentina Alaasam
- Virginia Tech, Department of Fish and Wildlife Conservation, Blacksburg, VA 24060, USA
| | - W Keith Ray
- Virginia Tech, Fralin Life Sciences Institute, Blacksburg, VA 24060, USA
| | - Richard F Helm
- Virginia Tech, Department of Biochemistry, Blacksburg, VA 24060, USA
| | - William A Hopkins
- Virginia Tech, Department of Fish and Wildlife Conservation, Blacksburg, VA 24060, USA
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2
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Bollinger KW, Müh U, Ocius KL, Apostolos AJ, Pires MM, Helm RF, Popham DL, Weiss DS, Ellermeier CD. Identification of a new family of peptidoglycan transpeptidases reveals atypical crosslinking is essential for viability in Clostridioides difficile. bioRxiv 2024:2024.03.14.584917. [PMID: 38559057 PMCID: PMC10980060 DOI: 10.1101/2024.03.14.584917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Clostridioides difficile, the leading cause of antibiotic-associated diarrhea, relies primarily on 3-3 crosslinks created by L,D-transpeptidases (LDTs) to fortify its peptidoglycan (PG) cell wall. This is unusual, as in most bacteria the vast majority of PG crosslinks are 4-3 crosslinks, which are created by penicillin-binding proteins (PBPs). Here we report the unprecedented observation that 3-3 crosslinking is essential for viability in C. difficile. We also report the discovery of a new family of LDTs that use a VanW domain to catalyze 3-3 crosslinking rather than a YkuD domain as in all previously known LDTs. Bioinformatic analyses indicate VanW domain LDTs are less common than YkuD domain LDTs and are largely restricted to Gram-positive bacteria. Our findings suggest that LDTs might be exploited as targets for antibiotics that kill C. difficile without disrupting the intestinal microbiota that is important for keeping C. difficile in check.
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Affiliation(s)
- Kevin W. Bollinger
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Ute Müh
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Karl L. Ocius
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
| | - Alexis J. Apostolos
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
- Present address: Haleon, 1211 Sherwood Ave, Richmond, VA 23220
| | - Marcos M. Pires
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
| | - Richard F. Helm
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA
| | - David L. Popham
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - David S. Weiss
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Graduate Program in Genetics, University of Iowa, Iowa City, IA USA
| | - Craig D. Ellermeier
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Graduate Program in Genetics, University of Iowa, Iowa City, IA USA
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3
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Sarasa-Buisan C, Nieves-Morión M, Arévalo S, Helm RF, Sevilla E, Luque I, Fillat MF. FurC (PerR) contributes to the regulation of peptidoglycan remodeling and intercellular molecular transfer in the cyanobacterium Anabaena sp. strain PCC 7120. mBio 2024; 15:e0323123. [PMID: 38334377 PMCID: PMC10936207 DOI: 10.1128/mbio.03231-23] [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: 12/04/2023] [Accepted: 01/09/2024] [Indexed: 02/10/2024] Open
Abstract
Microbial extracellular proteins and metabolites provide valuable information concerning how microbes adapt to changing environments. In cyanobacteria, dynamic acclimation strategies involve a variety of regulatory mechanisms, being ferric uptake regulator proteins as key players in this process. In the nitrogen-fixing cyanobacterium Anabaena sp. strain PCC 7120, FurC (PerR) is a global regulator that modulates the peroxide response and several genes involved in photosynthesis and nitrogen metabolism. To investigate the possible role of FurC in shaping the extracellular environment of Anabaena, the analysis of the extracellular metabolites and proteins of a furC-overexpressing variant was compared to that of the wild-type strain. There were 96 differentially abundant proteins, 78 of which were found for the first time in the extracellular fraction of Anabaena. While these proteins belong to different functional categories, most of them are predicted to be secreted or have a peripheral location. Several stress-related proteins, including PrxA, flavodoxin, and the Dps homolog All1173, accumulated in the exoproteome of furC-overexpressing cells, while decreased levels of FurA and a subset of membrane proteins, including several export proteins and amiC gene products, responsible for nanopore formation, were detected. Direct repression by FurC of some of those genes, including amiC1 and amiC2, could account for odd septal nanopore formation and impaired intercellular molecular transfer observed in the furC-overexpressing variant. Assessment of the exometabolome from both strains revealed the release of two peptidoglycan fragments in furC-overexpressing cells, namely 1,6-anhydro-N-acetyl-β-D-muramic acid (anhydroMurNAc) and its associated disaccharide (β-D-GlcNAc-(1-4)-anhydroMurNAc), suggesting alterations in peptidoglycan breakdown and recycling.IMPORTANCECyanobacteria are ubiquitous photosynthetic prokaryotes that can adapt to environmental stresses by modulating their extracellular contents. Measurements of the organization and composition of the extracellular milieu provide useful information about cyanobacterial adaptive processes, which can potentially lead to biomimetic approaches to stabilizing biological systems to adverse conditions. Anabaena sp. strain PCC 7120 is a multicellular, nitrogen-fixing cyanobacterium whose intercellular molecular exchange is mediated by septal junctions that traverse the septal peptidoglycan through nanopores. FurC (PerR) is an essential transcriptional regulator in Anabaena, which modulates the response to several stresses. Here, we show that furC-overexpressing cells result in a modified exoproteome and the release of peptidoglycan fragments. Phenotypically, important alterations in nanopore formation and cell-to-cell communication were observed. Our results expand the roles of FurC to the modulation of cell-wall biogenesis and recycling, as well as in intercellular molecular transfer.
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Affiliation(s)
- Cristina Sarasa-Buisan
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias e Instituto de Biocomputación y Física de Sistemas Complejos. Universidad de Zaragoza, Zaragoza, Spain
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Sevilla, Spain
| | - Mercedes Nieves-Morión
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Sevilla, Spain
| | - Sergio Arévalo
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Sevilla, Spain
| | - Richard F. Helm
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, USA
| | - Emma Sevilla
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias e Instituto de Biocomputación y Física de Sistemas Complejos. Universidad de Zaragoza, Zaragoza, Spain
| | - Ignacio Luque
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Sevilla, Spain
| | - María F. Fillat
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias e Instituto de Biocomputación y Física de Sistemas Complejos. Universidad de Zaragoza, Zaragoza, Spain
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4
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Farrell K, Auerbach A, Liu C, Martin K, Pareno M, Ray WK, Helm RF, Biase F, Jarome TJ. Sex-differences in proteasome-dependent K48-polyubiquitin signaling in the amygdala are developmentally regulated in rats. Biol Sex Differ 2023; 14:80. [PMID: 37950270 PMCID: PMC10638793 DOI: 10.1186/s13293-023-00566-z] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 11/06/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Sex differences have been observed in several brain regions for the molecular mechanisms involved in baseline (resting) and memory-related processes. The ubiquitin proteasome system (UPS) is a major protein degradation pathway in cells. Sex differences have been observed in lysine-48 (K48)-polyubiquitination, the canonical degradation mark of the UPS, both at baseline and during fear memory formation within the amygdala. Here, we investigated when, how, and why these baseline sex differences arise and whether both sexes require the K48-polyubiquitin mark for memory formation in the amygdala. METHODS We used a combination of molecular, biochemical and proteomic approaches to examine global and protein-specific K48-polyubiquitination and DNA methylation levels at a major ubiquitin coding gene (Uba52) at baseline in the amygdala of male and female rats before and after puberty to determine if sex differences were developmentally regulated. We then used behavioral and genetic approaches to test the necessity of K48-polyubiquitination in the amygdala for fear memory formation. RESULTS We observed developmentally regulated baseline differences in Uba52 methylation and total K48-polyubiquitination, with sexual maturity altering levels specifically in female rats. K48-polyubiquitination at specific proteins changed across development in both male and female rats, but sex differences were present regardless of age. Lastly, we found that genetic inhibition of K48-polyubiquitination in the amygdala of female, but not male, rats impaired fear memory formation. CONCLUSIONS These results suggest that K48-polyubiquitination differentially targets proteins in the amygdala in a sex-specific manner regardless of age. However, sexual maturity is important in the developmental regulation of K48-polyubiquitination levels in female rats. Consistent with these data, K48-polyubiquitin signaling in the amygdala is selectively required to form fear memories in female rats. Together, these data indicate that sex-differences in baseline K48-polyubiquitination within the amygdala are developmentally regulated, which could have important implications for better understanding sex-differences in molecular mechanisms involved in processes relevant to anxiety-related disorders such as post-traumatic stress disorder (PTSD).
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Affiliation(s)
- Kayla Farrell
- School of Animal Sciences, Virginia Polytechnic Institute and State University, 175 West Campus Dr., 2150 Litton-Reaves Hall, Blacksburg, VA, 24061, USA
| | - Aubrey Auerbach
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Catherine Liu
- School of Animal Sciences, Virginia Polytechnic Institute and State University, 175 West Campus Dr., 2150 Litton-Reaves Hall, Blacksburg, VA, 24061, USA
| | - Kiley Martin
- School of Neuroscience, Virginia Polytechnic Institute and State University, 175 West Campus Dr., 2150 Litton-Reaves Hall, Blacksburg, VA, 24061, USA
| | - Myasia Pareno
- School of Animal Sciences, Virginia Polytechnic Institute and State University, 175 West Campus Dr., 2150 Litton-Reaves Hall, Blacksburg, VA, 24061, USA
| | - W Keith Ray
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Richard F Helm
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Fernando Biase
- School of Animal Sciences, Virginia Polytechnic Institute and State University, 175 West Campus Dr., 2150 Litton-Reaves Hall, Blacksburg, VA, 24061, USA
| | - Timothy J Jarome
- School of Animal Sciences, Virginia Polytechnic Institute and State University, 175 West Campus Dr., 2150 Litton-Reaves Hall, Blacksburg, VA, 24061, USA.
- School of Neuroscience, Virginia Polytechnic Institute and State University, 175 West Campus Dr., 2150 Litton-Reaves Hall, Blacksburg, VA, 24061, USA.
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5
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Ni X, Murray NB, Archer-Hartmann S, Pepi LE, Helm RF, Azadi P, Hong P. Toward Automatic Inference of Glycan Linkages Using MS n and Machine Learning─Proof of Concept Using Sialic Acid Linkages. J Am Soc Mass Spectrom 2023; 34:2127-2135. [PMID: 37621000 PMCID: PMC10557947 DOI: 10.1021/jasms.3c00132] [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] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 08/10/2023] [Accepted: 08/15/2023] [Indexed: 08/26/2023]
Abstract
Glycosidic linkages in oligosaccharides play essential roles in determining their chemical properties and biological activities. MSn has been widely used to infer glycosidic linkages but requires a substantial amount of starting material, which limits its application. In addition, there is a lack of rigorous research on what MSn protocols are proper for characterizing glycosidic linkages. In this work, to deliver high-quality experimental data and analysis results, we propose a machine learning-based framework to establish appropriate MSn protocols and build effective data analysis methods. We demonstrate the proof-of-principle by applying our approach to elucidate sialic acid linkages (α2'-3' and α2'-6') in a set of sialyllactose standards and NIST sialic acid-containing N-glycans as well as identify several protocol configurations for producing high-quality experimental data. Our companion data analysis method achieves nearly 100% accuracy in classifying α2'-3' vs α2'-6' using MS5, MS4, MS3, or even MS2 spectra alone. The ability to determine glycosidic linkages using MS2 or MS3 is significant as it requires substantially less sample, enabling linkage analysis for quantity-limited natural glycans and synthesized materials, as well as shortens the overall experimental time. MS2 is also more amenable than MS3/4/5 to automation when coupled to direct infusion or LC-MS. Additionally, our method can predict the ratio of α2'-3' and α2'-6' in a mixture with 8.6% RMSE (root-mean-square error) across data sets using MS5 spectra. We anticipate that our framework will be generally applicable to analysis of other glycosidic linkages.
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Affiliation(s)
- Xinyi Ni
- Computer
Science, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Nathan B. Murray
- Complex
Carbohydrate Research Center, University
of Georgia, Athens, Georgia 30602, United States
| | | | - Lauren E. Pepi
- Complex
Carbohydrate Research Center, University
of Georgia, Athens, Georgia 30602, United States
| | - Richard F. Helm
- Department
of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Parastoo Azadi
- Complex
Carbohydrate Research Center, University
of Georgia, Athens, Georgia 30602, United States
| | - Pengyu Hong
- Computer
Science, Brandeis University, Waltham, Massachusetts 02453, United States
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6
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Farrell K, Musaus M, Auerbach A, Navabpour S, Ray WK, Helm RF, Jarome TJ. Proteasome-independent K63 polyubiquitination selectively regulates ATP levels and proteasome activity during fear memory formation in the female amygdala. Mol Psychiatry 2023; 28:2594-2605. [PMID: 37198264 PMCID: PMC10615704 DOI: 10.1038/s41380-023-02112-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/26/2023] [Accepted: 05/05/2023] [Indexed: 05/19/2023]
Abstract
Females are more likely than males to develop post-traumatic stress disorder (PTSD). However, the neurobiological mechanisms responsible for these sex differences remain elusive. The ubiquitin proteasome system (UPS) is involved in fear memory formation and implicated in PTSD development. Despite this, proteasome-independent functions of the UPS have rarely been studied in the brain. Here, using a combination of molecular, biochemical, proteomic, behavioral, and novel genetic approaches, we investigated the role of proteasome-independent lysine-63 (K63)-polyubiquitination, the second most abundant ubiquitin modification in cells, in the amygdala during fear memory formation in male and female rats. Only females had increased levels of K63-polyubiquitination targeting in the amygdala following fear conditioning, which targeted proteins involved in ATP synthesis and proteasome function. CRISPR-dCas13b-mediated knockdown of K63-polyubiquitination in the amygdala via editing of the K63 codon in the major ubiquitin gene, Ubc, impaired fear memory in females, but not males, and caused a reduction in learning-related increases in ATP levels and proteasome activity in the female amygdala. These results suggest that proteasome-independent K63-polyubiquitination is selectively involved in fear memory formation in the female amygdala, where it is involved in the regulation of ATP synthesis and proteasome activity following learning. This indicates the first link between proteasome-independent and proteasome-dependent UPS functions in the brain during fear memory formation. Importantly, these data are congruent with reported sex differences in PTSD development and may contribute to our understanding of why females are more likely to develop PTSD than males.
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Affiliation(s)
- Kayla Farrell
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Madeline Musaus
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Aubrey Auerbach
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Shaghayegh Navabpour
- Translational Biology, Medicine and Health Graduate Program, Virginia Polytechnic Institute and State University, Roanoke, VA, USA
| | - W Keith Ray
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Richard F Helm
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Timothy J Jarome
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.
- Translational Biology, Medicine and Health Graduate Program, Virginia Polytechnic Institute and State University, Roanoke, VA, USA.
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7
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Wooldridge R, Stone S, Pedraza A, Ray WK, Helm RF, Allen KD. The Chlamydia trachomatis p-aminobenzoate synthase CADD is a manganese-dependent oxygenase that uses its own amino acid residues as substrates. FEBS Lett 2023; 597:557-572. [PMID: 36647787 DOI: 10.1002/1873-3468.14573] [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: 09/11/2022] [Revised: 12/28/2022] [Accepted: 01/02/2023] [Indexed: 01/18/2023]
Abstract
CADD (chlamydia protein associating with death domains) is a p-aminobenzoate (pAB) synthase involved in a noncanonical route for tetrahydrofolate biosynthesis in Chlamydia trachomatis. Although previously implicated to employ a diiron cofactor, here, we show that pAB synthesis by CADD requires manganese and the physiological cofactor is most likely a heterodinuclear Mn/Fe cluster. Isotope-labeling experiments revealed that the two oxygen atoms in the carboxylic acid portion of pAB are derived from molecular oxygen. Further, mass spectrometry-based proteomic analyses of CADD-derived peptides demonstrated a glycine substitution at Tyr27, providing strong evidence that this residue is sacrificed for pAB synthesis. Additionally, Lys152 was deaminated and oxidized to aminoadipic acid, supporting its proposed role as a sacrificial amino group donor.
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Affiliation(s)
| | - Spenser Stone
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA
| | - Andrew Pedraza
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA
| | - W Keith Ray
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA
| | - Richard F Helm
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA
| | - Kylie D Allen
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA
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8
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Velander P, Wu L, Hildreth SB, Vogelaar NJ, Mukhopadhyay B, Helm RF, Zhang S, Xu B. Catechol-containing compounds are a broad class of protein aggregation inhibitors: Redox state is a key determinant of the inhibitory activities. Pharmacol Res 2022; 184:106409. [PMID: 35995346 PMCID: PMC10074477 DOI: 10.1016/j.phrs.2022.106409] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 07/20/2022] [Accepted: 08/17/2022] [Indexed: 12/30/2022]
Abstract
A range of neurodegenerative and related aging diseases, such as Alzheimer's disease and type 2 diabetes, are linked to toxic protein aggregation. Yet the mechanisms of protein aggregation inhibition by small molecule inhibitors remain poorly understood, in part because most protein targets of aggregation assembly are partially unfolded or intrinsically disordered, which hinders detailed structural characterization of protein-inhibitor complexes and structural-based inhibitor design. Herein we employed a parallel small molecule library-screening approach to identify inhibitors against three prototype amyloidogenic proteins in neurodegeneration and related proteinopathies: amylin, Aβ and tau. One remarkable class of inhibitors identified from these screens against different amyloidogenic proteins was catechol-containing compounds and redox-related quinones/anthraquinones. Secondary assays validated most of the identified inhibitors. In vivo efficacy evaluation of a selected catechol-containing compound, rosmarinic acid, demonstrated its strong mitigating effects of amylin amyloid deposition and related diabetic pathology in transgenic HIP rats. Further systematic investigation of selected class of inhibitors under aerobic and anaerobic conditions revealed that the redox state of the broad class of catechol-containing compounds is a key determinant of the amyloid inhibitor activities. The molecular insights we gained not only explain why a large number of catechol-containing polyphenolic natural compounds, often enriched in healthy diet, have anti-neurodegeneration and anti-aging activities, but also could guide the rational design of therapeutic or nutraceutical strategies to target a broad range of neurodegenerative and related aging diseases.
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Affiliation(s)
- Paul Velander
- Department of Biochemistry, Virginia Polytechnic Institute & State University, Blacksburg, VA 24061, USA
| | - Ling Wu
- Department of Biochemistry, Virginia Polytechnic Institute & State University, Blacksburg, VA 24061, USA; BRITE Research Institute and Department of Pharmaceutical Sciences, North Carolina Central University, Durham, NC 27707, USA; Affiliated Faculty, Duke/UNC Alzheimer's Disease Research Center, Durham, NC 27710, USA
| | - Sherry B Hildreth
- Department of Biochemistry, Virginia Polytechnic Institute & State University, Blacksburg, VA 24061, USA
| | - Nancy J Vogelaar
- Department of Biochemistry, Virginia Polytechnic Institute & State University, Blacksburg, VA 24061, USA; Center for Drug Discovery, Virginia Polytechnic Institute & State University, Blacksburg, VA 24061, USA
| | - Biswarup Mukhopadhyay
- Department of Biochemistry, Virginia Polytechnic Institute & State University, Blacksburg, VA 24061, USA
| | - Richard F Helm
- Department of Biochemistry, Virginia Polytechnic Institute & State University, Blacksburg, VA 24061, USA
| | - Shijun Zhang
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Bin Xu
- Department of Biochemistry, Virginia Polytechnic Institute & State University, Blacksburg, VA 24061, USA; Center for Drug Discovery, Virginia Polytechnic Institute & State University, Blacksburg, VA 24061, USA; School of Neuroscience, Virginia Polytechnic Institute & State University, Blacksburg, VA 24061, USA; BRITE Research Institute and Department of Pharmaceutical Sciences, North Carolina Central University, Durham, NC 27707, USA; Affiliated Faculty, Duke/UNC Alzheimer's Disease Research Center, Durham, NC 27710, USA.
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9
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Gustin A, Navabpour S, Farrell K, Martin K, DuVall J, Keith Ray W, Helm RF, Jarome TJ. Protein SUMOylation is a sex-specific regulator of fear memory formation in the amygdala. Behav Brain Res 2022; 430:113928. [PMID: 35597476 PMCID: PMC10431910 DOI: 10.1016/j.bbr.2022.113928] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 12/08/2021] [Revised: 04/11/2022] [Accepted: 05/12/2022] [Indexed: 11/25/2022]
Abstract
Strong evidence has implicated ubiquitin signaling in the process of fear memory formation. While less abundant than ubiquitination, evidence suggests that protein SUMOylation may also be involved in fear memory formation in neurons. However, the importance of amygdala protein SUMOylation in fear memory formation has never been directly examined. Furthermore, while recent evidence indicates that males and females differ significantly in the requirement for ubiquitin signaling during fear memory formation, whether sex differences also exist in the importance of protein SUMOylation to this process remains unknown. Here we found that males and females differ in the requirement for protein SUMOylation in the amygdala during fear memory formation. Western blot analysis revealed that while females had higher resting levels of SUMOylation, both sexes showed global increases following fear conditioning. However, SUMOylation-specific proteomic analysis revealed that only females have increased targeting of individual proteins by SUMOylation following fear conditioning, some of which were heat shock proteins. This suggests that protein SUMOylation is more robustly engaged in the amygdala of females following fear conditioning. In vivo siRNA mediated knockdown of Ube2i, the coding gene for the essential E2 ligase for SUMOylation conjugation, in the amygdala impaired fear memory in males without any effect in females. Importantly, higher siRNA concentrations than what was needed to impair memory in males reduced Ube2i levels in the amygdala of females but resulted in an increase in SUMOylation levels, suggesting a compensatory effect in females that was not observed in males. Collectively, these data reveal a novel, sex-specific role for protein SUMOylation in the amygdala during fear memory formation and expand our understanding of how ubiquitin-like signaling regulates memory formation.
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Affiliation(s)
- Aspen Gustin
- Department of Animal and Poultry Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Shaghayegh Navabpour
- Fralin Biomedical Research Institute, Department of Translational Biology, Medicine and Health, Virginia Polytechnic Institute and State University, Roanoke, VA, USA
| | - Kayla Farrell
- Department of Animal and Poultry Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Kiley Martin
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Jessica DuVall
- Department of Animal and Poultry Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - W Keith Ray
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Richard F Helm
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Timothy J Jarome
- Department of Animal and Poultry Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA; Fralin Biomedical Research Institute, Department of Translational Biology, Medicine and Health, Virginia Polytechnic Institute and State University, Roanoke, VA, USA; School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.
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10
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Wu L, Wang Z, Lad S, Gilyazova N, Dougharty DT, Marcus M, Henderson F, Ray WK, Siedlak S, Li J, Helm RF, Zhu X, Bloom GS, Wang SHJ, Zou WQ, Xu B. Selective Detection of Misfolded Tau From Postmortem Alzheimer's Disease Brains. Front Aging Neurosci 2022; 14:945875. [PMID: 35936779 PMCID: PMC9352240 DOI: 10.3389/fnagi.2022.945875] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 06/21/2022] [Indexed: 01/04/2023] Open
Abstract
Tau aggregates are present in multiple neurodegenerative diseases known as "tauopathies," including Alzheimer's disease, Pick's disease, progressive supranuclear palsy, and corticobasal degeneration. Such misfolded tau aggregates are therefore potential sources for selective detection and biomarker discovery. Six human tau isoforms present in brain tissues and both 3R and 4R isoforms have been observed in the neuronal inclusions. To develop selective markers for AD and related rare tauopathies, we first used an engineered tau protein fragment 4RCF as the substrate for ultrasensitive real-time quaking-induced conversion analyses (RT-QuIC). We showed that misfolded tau from diseased AD and other tauopathy brains were able to seed recombinant 4RCF substrate. We further expanded to use six individual recombinant tau isoforms as substrates to amplify misfolded tau seeds from AD brains. We demonstrated, for the first time to our knowledge, that misfolded tau from the postmortem AD brain tissues was able to specifically seed all six full-length human tau isoforms. Our results demonstrated that RT-QuIC analysis can discriminate AD and other tauopathies from non-AD normal controls. We further uncovered that 3R-tau isoforms displayed significantly faster aggregation kinetics than their 4R-tau counterparts under conditions of both no seeding and seeding with AD brain homogenates. In summary, our work offers potential new avenues of misfolded tau detection as potential biomarkers for diagnosis of AD and related tauopathies and provides new insights into isoform-specific human tau aggregation.
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Affiliation(s)
- Ling Wu
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute and Technology Enterprise (BRITE), North Carolina Central University, Durham, NC, United States
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Zerui Wang
- Department of Pathology, Case Western Reserve University, Cleveland, OH, United States
| | - Shradha Lad
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Nailya Gilyazova
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute and Technology Enterprise (BRITE), North Carolina Central University, Durham, NC, United States
| | - Darren T. Dougharty
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Madeleine Marcus
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Frances Henderson
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - W. Keith Ray
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Sandra Siedlak
- Department of Pathology, Case Western Reserve University, Cleveland, OH, United States
| | - Jianyong Li
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Richard F. Helm
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Xiongwei Zhu
- Department of Pathology, Case Western Reserve University, Cleveland, OH, United States
| | - George S. Bloom
- Departments of Biology, Cell Biology, and Neuroscience, University of Virginia, Charlottesville, VA, United States
| | - Shih-Hsiu J. Wang
- Department of Pathology and Neurology, Duke University Medical Center, Durham, NC, United States
| | - Wen-Quan Zou
- Department of Pathology, Case Western Reserve University, Cleveland, OH, United States
| | - Bin Xu
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute and Technology Enterprise (BRITE), North Carolina Central University, Durham, NC, United States
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
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11
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Galligan TM, Helm RF, Case BF, Bodinof Jachowski CM, Frazier CL, Alaasam V, Hopkins WA. Pre-breeding androgen and glucocorticoid profiles in the eastern hellbender salamander (Cryptobranchus alleganiensis alleganiensis). Gen Comp Endocrinol 2021; 313:113899. [PMID: 34499909 DOI: 10.1016/j.ygcen.2021.113899] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 08/10/2021] [Accepted: 09/03/2021] [Indexed: 11/28/2022]
Abstract
Seasonally breeding species exhibit cyclical changes in circulating steroid hormone profiles that correspond with changes to their reproductive behavior and ecology. Such information is critical to the conservation of imperiled and data-deficient species, such as the eastern hellbender salamander (Cryptobranchus alleganiensis alleganiensis). We determined changes in plasma testosterone (T), dihydrotestosterone (DHT), 11-ketotestosterone (11-KT), 11-ketoandrostenedione (11-KA), dehydroepiandrosterone (DHEA), cortisol, corticosterone, and progesterone (P4) during a four-month period preceding breeding in adult male and female eastern hellbenders. This pre-breeding period is characterized by increased diel movement and aggression by both sexes, follicular development and yolk production in females, and sperm production, territoriality, and nest site establishment in males. In both males and females, we observed a progressive increase in circulating T and DHT during the pre-reproductive season, both peaking in August (17 days before breeding), but concentrations of both hormones were higher in males. Conversely, 11-KT was higher in females, but did not vary significantly by date. These results suggest that T and DHT are the predominant androgens in eastern hellbenders and are likely important regulators of reproductive processes in both males and females. The detection of significant quantities of DHT and 11-KT in females is particularly interesting, considering that unlike T, neither of these androgens can be converted to estrogens. Therefore, it seems possible that aggression or some aspect of reproduction in the female eastern hellbender may be directly mediated by androgen signaling. Baseline cortisol did not vary throughout the pre-breeding period but was higher in females than males, and also became highly variable in females leading up to breeding. Progesterone, 11-KA, DHEA, and corticosterone were rarely or never detected, and thus, do not appear to be important during the pre-reproductive season. This study provides a physiological framework for future studies of hellbender reproductive biology, which could ultimately be important for their conservation.
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Affiliation(s)
- Thomas M Galligan
- Virginia Tech, Department of Fish and Wildlife Conservation, Blacksburg, VA USA 24060, USA; Environmental Working Group, 1436 U St. NW #100, Washington, DC 20009, USA.
| | - Richard F Helm
- Virginia Tech, Department of Biochemistry, Blacksburg, VA USA 24060, USA
| | - Brian F Case
- Virginia Tech, Department of Fish and Wildlife Conservation, Blacksburg, VA USA 24060, USA
| | - Catherine M Bodinof Jachowski
- Virginia Tech, Department of Fish and Wildlife Conservation, Blacksburg, VA USA 24060, USA; Forestry and Environmental Conservation Department, Clemson University, Clemson, SC 29634, USA
| | - Clara L Frazier
- Virginia Tech, Department of Biochemistry, Blacksburg, VA USA 24060, USA
| | - Valentina Alaasam
- Virginia Tech, Department of Fish and Wildlife Conservation, Blacksburg, VA USA 24060, USA; Ecology, Evolution, and Conservation Biology, University Nevada-Reno, Reno, NV 89557, USA
| | - William A Hopkins
- Virginia Tech, Department of Fish and Wildlife Conservation, Blacksburg, VA USA 24060, USA
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12
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Farrell K, Musaus M, Navabpour S, Martin K, Ray WK, Helm RF, Jarome TJ. Proteomic Analysis Reveals Sex-Specific Protein Degradation Targets in the Amygdala During Fear Memory Formation. Front Mol Neurosci 2021; 14:716284. [PMID: 34658783 PMCID: PMC8511838 DOI: 10.3389/fnmol.2021.716284] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 09/01/2021] [Indexed: 11/25/2022] Open
Abstract
Ubiquitin-proteasome mediated protein degradation has been widely implicated in fear memory formation in the amygdala. However, to date, the protein targets of the proteasome remain largely unknown, limiting our understanding of the functional significance for protein degradation in fear memory formation. Additionally, whether similar proteins are targeted by the proteasome between sexes has yet to be explored. Here, we combined a degradation-specific K48 Tandem Ubiquitin Binding Entity (TUBE) with liquid chromatography mass spectrometry (LC/MS) to identify the target substrates of the protein degradation process in the amygdala of male and female rats following contextual fear conditioning. We found that males (43) and females (77) differed in the total number of proteins that had significant changes in K48 polyubiquitin targeting in the amygdala following fear conditioning. Many of the identified proteins (106) had significantly reduced levels in the K48-purified samples 1 h after fear conditioning, suggesting active degradation of the substrate due to learning. Interestingly, only 3 proteins overlapped between sexes, suggesting that targets of the protein degradation process may be sex-specific. In females, many proteins with altered abundance in the K48-purified samples were involved in vesicle transport or are associated with microtubules. Conversely, in males, proteins involved in the cytoskeleton, ATP synthesis and cell signaling were found to have significantly altered abundance. Only 1 protein had an opposite directional change in abundance between sexes, LENG1, which was significantly enhanced in males while lower in females. This suggests a more rapid degradation of this protein in females during fear memory formation. Interestingly, GFAP, a critical component of astrocyte structure, was a target of K48 polyubiquitination in both males and females, indicating that protein degradation is likely occurring in astrocytes following fear conditioning. Western blot assays revealed reduced levels of these target substrates following fear conditioning in both sexes, confirming that the K48 polyubiquitin was targeting these proteins for degradation. Collectively, this study provides strong evidence that sex differences exist in the protein targets of the degradation process in the amygdala following fear conditioning and critical information regarding how ubiquitin-proteasome mediated protein degradation may contribute to fear memory formation in the brain.
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Affiliation(s)
- Kayla Farrell
- Department of Animal and Poultry Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Madeline Musaus
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Shaghayegh Navabpour
- Department of Translational Biology, Medicine and Health, Virginia Polytechnic Institute and State University, Roanoke, VA, United States
| | - Kiley Martin
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - W Keith Ray
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Richard F Helm
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Timothy J Jarome
- Department of Animal and Poultry Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States.,School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States.,Department of Translational Biology, Medicine and Health, Virginia Polytechnic Institute and State University, Roanoke, VA, United States
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13
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Martin K, Musaus M, Navabpour S, Gustin A, Ray WK, Helm RF, Jarome TJ. Females, but not males, require protein degradation in the hippocampus for contextual fear memory formation. ACTA ACUST UNITED AC 2021; 28:248-253. [PMID: 34266989 PMCID: PMC8284313 DOI: 10.1101/lm.053429.121] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/07/2021] [Indexed: 11/30/2022]
Abstract
Strong evidence supports a role for protein degradation in fear memory formation. However, these data have been largely done in only male animals. Here, we found that following contextual fear conditioning, females, but not males, had increased levels of proteasome activity and K48 polyubiquitin protein targeting in the dorsal hippocampus, the latter of which occurred at chaperones or RNA processing proteins. In vivo CRISPR–dCas9-mediated repression of protein degradation in the dorsal hippocampus impaired contextual fear memory in females, but not males. These results suggest a sex-specific role for protein degradation in the hippocampus during the consolidation of a contextual fear memory.
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Affiliation(s)
- Kiley Martin
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Madeline Musaus
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Shaghayegh Navabpour
- Fralin Biomedical Research Institute, Department of Translational Biology, Medicine, and Health, Virginia Polytechnic Institute and State University, Roanoke, Virginia 24016, USA
| | - Aspen Gustin
- Department of Animal and Poultry Science, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - W Keith Ray
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Richard F Helm
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Timothy J Jarome
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA.,Fralin Biomedical Research Institute, Department of Translational Biology, Medicine, and Health, Virginia Polytechnic Institute and State University, Roanoke, Virginia 24016, USA.,Department of Animal and Poultry Science, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
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14
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Musaus M, Farrell K, Navabpour S, Ray WK, Helm RF, Jarome TJ. Sex-Specific Linear Polyubiquitination Is a Critical Regulator of Contextual Fear Memory Formation. Front Behav Neurosci 2021; 15:709392. [PMID: 34305548 PMCID: PMC8298817 DOI: 10.3389/fnbeh.2021.709392] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 06/22/2021] [Indexed: 12/27/2022] Open
Abstract
Strong evidence supports that protein ubiquitination is a critical regulator of fear memory formation. However, as this work has focused on protein degradation, it is currently unknown whether polyubiquitin modifications that are independent of the proteasome are involved in learning-dependent synaptic plasticity. Here, we present the first evidence that atypical linear (M1) polyubiquitination, the only ubiquitin chain that does not occur at a lysine site and is largely independent of the proteasome, is critically involved in contextual fear memory formation in the amygdala in a sex-specific manner. Using immunoblot and unbiased proteomic analyses, we found that male (49) and female (14) rats both had increased levels of linear polyubiquitinated substrates following fear conditioning, though none of these protein targets overlapped between sexes. In males, target protein functions involved cell junction and axonal guidance signaling, while in females the primary target was Adiponectin A, a critical regulator of neuroinflammation, synaptic plasticity, and memory, suggesting sex-dependent functional roles for linear polyubiquitination during fear memory formation. Consistent with these increases, in vivo siRNA-mediated knockdown of Rnf31, an essential component of the linear polyubiquitin E3 complex LUBAC, in the amygdala impaired contextual fear memory in both sexes without affecting memory retrieval. Collectively, these results provide the first evidence that proteasome-independent linear polyubiquitination is a critical regulator of fear memory formation, expanding the potential roles of ubiquitin-signaling in learning-dependent synaptic plasticity. Importantly, our data identify a novel sex difference in the functional role of, but not a requirement for, linear polyubiquitination in fear memory formation.
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Affiliation(s)
- Madeline Musaus
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Kayla Farrell
- Department of Animal and Poultry Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Shaghayegh Navabpour
- Department of Translational Biology, Medicine and Health, Virginia Polytechnic Institute and State University, Roanoke, VA, United States
| | - W. Keith Ray
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Richard F. Helm
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Timothy J. Jarome
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
- Department of Animal and Poultry Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
- Department of Translational Biology, Medicine and Health, Virginia Polytechnic Institute and State University, Roanoke, VA, United States
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15
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Schneider GF, Salazar D, Hildreth SB, Helm RF, Whitehead SR. Comparative Metabolomics of Fruits and Leaves in a Hyperdiverse Lineage Suggests Fruits Are a Key Incubator of Phytochemical Diversification. Front Plant Sci 2021; 12:693739. [PMID: 34527005 PMCID: PMC8435686 DOI: 10.3389/fpls.2021.693739] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 07/30/2021] [Indexed: 05/05/2023]
Abstract
Interactions between plants and leaf herbivores have long been implicated as the major driver of plant secondary metabolite diversity. However, other plant-animal interactions, such as those between fruits and frugivores, may also be involved in phytochemical diversification. Using 12 species of Piper, we conducted untargeted metabolomics and molecular networking with extracts of fruits and leaves. We evaluated organ-specific secondary metabolite composition and compared multiple dimensions of phytochemical diversity across organs, including richness, structural complexity, and variability across samples at multiple scales within and across species. Plant organ identity, species identity, and the interaction between the two all significantly influenced secondary metabolite composition. Leaves and fruit shared a majority of compounds, but fruits contained more unique compounds and had higher total estimated chemical richness. While the relative levels of chemical richness and structural complexity across organs varied substantially across species, fruit diversity exceeded leaf diversity in more species than the reverse. Furthermore, the variance in chemical composition across samples was higher for fruits than leaves. By documenting a broad pattern of high phytochemical diversity in fruits relative to leaves, this study lays groundwork for incorporating fruit into a comprehensive and integrative understanding of the ecological and evolutionary factors shaping secondary metabolite composition at the whole-plant level.
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Affiliation(s)
- Gerald F. Schneider
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
- Department of Biology, Utah State University, Logan, UT, United States
- *Correspondence: Gerald F. Schneider,
| | - Diego Salazar
- Department of Biological Sciences, International Center for Tropical Botany, Florida International University, Miami, FL, United States
| | - Sherry B. Hildreth
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
- Department of Biochemistry, Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Richard F. Helm
- Department of Biochemistry, Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Susan R. Whitehead
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
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16
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DeHart TG, Kushelman MR, Hildreth SB, Helm RF, Jutras BL. The unusual cell wall of the Lyme disease spirochaete Borrelia burgdorferi is shaped by a tick sugar. Nat Microbiol 2021; 6:1583-1592. [PMID: 34819646 PMCID: PMC8612929 DOI: 10.1038/s41564-021-01003-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 10/20/2021] [Indexed: 01/10/2023]
Abstract
Peptidoglycan-a mesh sac of glycans that are linked by peptides-is the main component of bacterial cell walls. Peptidoglycan provides structural strength, protects cells from osmotic pressure and contributes to shape. All bacterial glycans are repeating disaccharides of N-acetylglucosamine (GlcNAc) β-(1-4)-linked to N-acetylmuramic acid (MurNAc). Borrelia burgdorferi, the tick-borne Lyme disease pathogen, produces glycan chains in which MurNAc is occasionally replaced with an unknown sugar. Nuclear magnetic resonance, liquid chromatography-mass spectroscopy and genetic analyses show that B. burgdorferi produces glycans that contain GlcNAc-GlcNAc. This unusual disaccharide is chitobiose, a component of its chitinous tick vector. Mutant bacteria that are auxotrophic for chitobiose have altered morphology, reduced motility and cell envelope defects that probably result from producing peptidoglycan that is stiffer than that in wild-type bacteria. We propose that the peptidoglycan of B. burgdorferi probably evolved by adaptation to obligate parasitization of a tick vector, resulting in a biophysical cell-wall alteration to withstand the atypical torque associated with twisting motility.
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Affiliation(s)
- Tanner G. DeHart
- grid.438526.e0000 0001 0694 4940Department of Biochemistry, Virginia Tech, Blacksburg, VA USA ,grid.438526.e0000 0001 0694 4940Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA USA
| | - Mara R. Kushelman
- grid.438526.e0000 0001 0694 4940Department of Biochemistry, Virginia Tech, Blacksburg, VA USA ,grid.438526.e0000 0001 0694 4940Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA USA
| | - Sherry B. Hildreth
- grid.438526.e0000 0001 0694 4940Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA USA
| | - Richard F. Helm
- grid.438526.e0000 0001 0694 4940Department of Biochemistry, Virginia Tech, Blacksburg, VA USA ,grid.438526.e0000 0001 0694 4940Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA USA
| | - Brandon L. Jutras
- grid.438526.e0000 0001 0694 4940Department of Biochemistry, Virginia Tech, Blacksburg, VA USA ,grid.438526.e0000 0001 0694 4940Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA USA ,grid.438526.e0000 0001 0694 4940Molecular and Cellular Biology, Virginia Tech, Blacksburg, VA USA ,grid.438526.e0000 0001 0694 4940Translational Biology, Medicine, and Health, Virginia Tech, Blacksburg, VA USA ,grid.438526.e0000 0001 0694 4940Center for Emerging, Zoonotic and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, VA USA
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17
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Compton KK, Hildreth SB, Helm RF, Scharf BE. An Updated Perspective on Sinorhizobium meliloti Chemotaxis to Alfalfa Flavonoids. Front Microbiol 2020; 11:581482. [PMID: 33193213 PMCID: PMC7644916 DOI: 10.3389/fmicb.2020.581482] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 09/30/2020] [Indexed: 12/25/2022] Open
Abstract
The symbiotic interaction between leguminous plants and their cognate rhizobia allows for the fixation of gaseous dinitrogen into bioavailable ammonia. The perception of host-derived flavonoids is a key initial step for the signaling events that must occur preceding the formation of the nitrogen-fixing organ. Past work investigating chemotaxis – the directed movement of bacteria through chemical gradients – of Bradyrhizobium japonicum, Rhizobium leguminosarum, and Rhizobium meliloti discovered chemotaxis to various organic compounds, but focused on chemotaxis to flavonoids because of their relevance to the symbiosis biochemistry. The current work sought to replicate and further examine Sinorhizobium (Ensifer) meliloti chemotaxis to the flavonoids previously thought to act as the principal attractant molecules prior to the initial signaling stage. Exudate from germinating alfalfa seedlings was analyzed for composition and quantities of different flavonoid compounds using mass spectrometry. The abundance of four prevalent flavonoids in germinating alfalfa seed exudates (SEs) was at a ratio of 200:5:5:1 for hyperoside, luteolin, luteolin-7-glucoside, and chrysoeriol. Using quantitative chemotaxis capillary assays, we did not detect chemotaxis of motile S. meliloti cells to these, and two other flavonoids identified in seed exudates. In support of these findings, the flavonoid fraction of seed exudates was found to be an insignificant attractant relative to the more hydrophilic fraction. Additionally, we observed that cosolvents commonly used to dissolve flavonoids confound the results. We propose that the role flavonoids play in S. meliloti chemotaxis is insignificant relative to other components released by alfalfa seeds.
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Affiliation(s)
- K Karl Compton
- Department of Biological Sciences, Life Sciences I, Virginia Tech, Blacksburg, VA, United States
| | - Sherry B Hildreth
- Department of Biological Sciences, Life Sciences I, Virginia Tech, Blacksburg, VA, United States
| | - Richard F Helm
- Department of Biochemistry, Fralin Life Science Institute, Virginia Tech, Blacksburg, VA, United States
| | - Birgit E Scharf
- Department of Biological Sciences, Life Sciences I, Virginia Tech, Blacksburg, VA, United States
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18
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Arapov TD, Saldaña RC, Sebastian AL, Ray WK, Helm RF, Scharf BE. Cellular Stoichiometry of Chemotaxis Proteins in Sinorhizobium meliloti. J Bacteriol 2020; 202:e00141-20. [PMID: 32393521 PMCID: PMC7317046 DOI: 10.1128/jb.00141-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 03/18/2020] [Accepted: 05/05/2020] [Indexed: 11/20/2022] Open
Abstract
Chemotaxis systems enable microbes to sense their immediate environment, moving toward beneficial stimuli and away from those that are harmful. In an effort to better understand the chemotaxis system of Sinorhizobium meliloti, a symbiont of the legume alfalfa, the cellular stoichiometries of all ten chemotaxis proteins in S. meliloti were determined. A combination of quantitative immunoblot and mass spectrometry revealed that the protein stoichiometries in S. meliloti varied greatly from those in Escherichia coli and Bacillus subtilis To compare protein ratios to other systems, values were normalized to the central kinase CheA. All S. meliloti chemotaxis proteins exhibited increased ratios to various degrees. The 10-fold higher molar ratio of adaptor proteins CheW1 and CheW2 to CheA might result in the formation of rings in the chemotaxis array that consist of only CheW instead of CheA and CheW in a 1:1 ratio. We hypothesize that the higher ratio of CheA to the main response regulator CheY2 is a consequence of the speed-variable motor in S. meliloti, instead of a switch-type motor. Similarly, proteins involved in signal termination are far more abundant in S. meliloti, which utilizes a phosphate sink mechanism based on CheA retrophosphorylation to inactivate the motor response regulator versus CheZ-catalyzed dephosphorylation as in E. coli and B. subtilis Finally, the abundance of CheB and CheR, which regulate chemoreceptor methylation, was increased compared to CheA, indicative of variations in the adaptation system of S. meliloti Collectively, these results mark significant differences in the composition of bacterial chemotaxis systems.IMPORTANCE The symbiotic soil bacterium Sinorhizobium meliloti contributes greatly to host-plant growth by fixing atmospheric nitrogen. The provision of nitrogen as ammonium by S. meliloti leads to increased biomass production of its legume host alfalfa and diminishes the use of environmentally harmful chemical fertilizers. To better understand the role of chemotaxis in host-microbe interaction, a comprehensive catalogue of the bacterial chemotaxis system is vital, including its composition, function, and regulation. The stoichiometry of chemotaxis proteins in S. meliloti has very few similarities to the systems in Escherichia coli and Bacillus subtilis In addition, total amounts of proteins are significantly lower. S. meliloti exhibits a chemotaxis system distinct from known models by incorporating new proteins as exemplified by the phosphate sink mechanism.
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Affiliation(s)
- Timofey D Arapov
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | | | - Amanda L Sebastian
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - W Keith Ray
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, USA
| | - Richard F Helm
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, USA
| | - Birgit E Scharf
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
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Hopkins WA, DuRant SE, Beck ML, Ray WK, Helm RF, Romero LM. Cortisol is the predominant glucocorticoid in the giant paedomorphic hellbender salamander (Cryptobranchus alleganiensis). Gen Comp Endocrinol 2020; 285:113267. [PMID: 31491375 DOI: 10.1016/j.ygcen.2019.113267] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/19/2019] [Accepted: 09/01/2019] [Indexed: 11/20/2022]
Abstract
Corticosterone is widely regarded to be the predominant glucocorticoid produced in amphibians. However, we recently described unusually low baseline and stress-induced corticosterone profiles in eastern hellbenders (Cryptobranchus alleganiensis alleganiensis), a giant, fully aquatic salamander. Here, we hypothesized that hellbenders might also produce cortisol, the predominant glucocorticoid used by fishes and non-rodent mammals. To test our hypothesis, we collected plasma samples in two field experiments and analyzed them using multiple analytical techniques to determine how plasma concentrations of cortisol and corticosterone co-varied after 1) physical restraint and 2) injection with adrenocorticotropic hormone (ACTH), the pituitary hormone responsible for triggering the release of glucocorticoids from amphibian interrenal glands. Using liquid chromatography-mass spectrometry, we found that baseline and restraint-induced plasma concentrations of cortisol were more than five times those of corticosterone. We then demonstrated that plasma concentrations of both glucocorticoids increased in response to ACTH in a dose-dependent manner, but cortisol concentrations were consistently higher (up to 10-fold) than corticosterone. Cortisol and corticosterone concentrations were not correlated with one another at basal or induced conditions. The extremely low plasma concentrations of corticosterone in hellbenders suggests that corticosterone could simply be a byproduct of cortisol production, and raises questions as to whether corticosterone has any distinct physiological function in hellbenders. Our results indicate that hellbenders produce cortisol as their predominant glucocorticoid, supporting a small and inconclusive body of literature indicating that some other amphibians may produce appreciable quantities of cortisol. We hypothesize that the use of cortisol by hellbenders could be an adaptation to their fully aquatic life history due to cortisol's ability to fulfill both mineralocorticoid and glucocorticoid functions, similar to its functions in fishes. Given the large number of amphibian species that are fully aquatic or have aquatic life stages, we suggest that the broadly held assumption that corticosterone is the predominant glucocorticoid in all amphibians requires further scrutiny. Ultimately, multi-species tests of this assumption will reveal the ecological factors that influenced the evolution of endocrine adaptations among amphibian lineages, and may provide insight into convergent evolution of endocrine traits in paedomorphic species.
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Affiliation(s)
- William A Hopkins
- Dept of Fish and Wildlife Conservation, Virginia Tech, Blacksburg, VA 24061, USA.
| | - Sarah E DuRant
- Dept of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Michelle L Beck
- Dept of Fish and Wildlife Conservation, Virginia Tech, Blacksburg, VA 24061, USA; Dept. of Biology, Rivier University, Nashua, NH 03060, USA
| | - W Keith Ray
- Dept of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
| | - Richard F Helm
- Dept of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
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20
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Watkinson JI, Bowerman PA, Crosby KC, Hildreth SB, Helm RF, Winkel BSJ. Identification of MOS9 as an interaction partner for chalcone synthase in the nucleus. PeerJ 2018; 6:e5598. [PMID: 30258711 PMCID: PMC6151112 DOI: 10.7717/peerj.5598] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 08/17/2018] [Indexed: 01/12/2023] Open
Abstract
Plant flavonoid metabolism has served as a platform for understanding a range of fundamental biological phenomena, including providing some of the early insights into the subcellular organization of metabolism. Evidence assembled over the past three decades points to the organization of the component enzymes as a membrane-associated complex centered on the entry-point enzyme, chalcone synthase (CHS), with flux into branch pathways controlled by competitive protein interactions. Flavonoid enzymes have also been found in the nucleus in a variety of plant species, raising the possibility of alternative, or moonlighting functions for these proteins in this compartment. Here, we present evidence that CHS interacts with MOS9, a nuclear-localized protein that has been linked to epigenetic control of R genes that mediate effector-triggered immunity. Overexpression of MOS9 results in a reduction of CHS transcript levels and a metabolite profile that substantially intersects with the effects of a null mutation in CHS. These results suggest that the MOS9-CHS interaction may point to a previously-unknown mechanism for controlling the expression of the highly dynamic flavonoid pathway.
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Affiliation(s)
- Jonathan I Watkinson
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA
| | - Peter A Bowerman
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA.,BASF Plant Science LP, Research Triangle Park, NC, USA
| | - Kevin C Crosby
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA.,Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Sherry B Hildreth
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA.,Department of Biochemistry, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA
| | - Richard F Helm
- Department of Biochemistry, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA
| | - Brenda S J Winkel
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA
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21
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Lapierre C, Voxeur A, Karlen SD, Helm RF, Ralph J. Evaluation of Feruloylated and p-Coumaroylated Arabinosyl Units in Grass Arabinoxylans by Acidolysis in Dioxane/Methanol. J Agric Food Chem 2018; 66:5418-5424. [PMID: 29763561 DOI: 10.1021/acs.jafc.8b01618] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The arabinosyl side chains of grass arabinoxylans are partially acylated by p-coumarate ( pCA) and ferulate (FA). These aromatic side chains can cross-couple wall polymers resulting in modulation of cell wall physical properties. The determination of p-coumaroylated and feruloylated arabinose units has been the target of analytical efforts with trifluoroacetic acid hydrolysis the standard method to release feruloylated and p-coumaroylated arabinose units from arabinoxylans. Herein, we report on a more robust method to measure these acylated units. Acidolysis of extractive-free grass samples in a dioxane/methanol/aqueous 2 M HCl mixture provided the methyl 5- O- p-coumaroyl- and 5- O-feruloyl-l-arabinofuranoside anomers ( pCA-MeAra and FA-MeAra). These conjugates were readily analyzed by liquid chromatography combined with both UV and MS detection. The method revealed the variability of the relative acylation of arabinose units by pCA or FA in grass cell walls. This methodology will permit delineation of hydroxycinnamate acylation patterns in arabinoxylans.
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Affiliation(s)
- Catherine Lapierre
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS , Université Paris-Saclay , 78000 Versailles , France
| | - Aline Voxeur
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS , Université Paris-Saclay , 78000 Versailles , France
| | - Steven D Karlen
- Department of Biochemistry, and The Department of Energy's Great Lakes Bioenergy Research Center, The Wisconsin Energy Institute , University of Wisconsin , Madison , Wisconsin 53726 , United States
| | - Richard F Helm
- Department of Biochemistry , Virginia Tech , Blacksburg , Virginia 24061 , United States
| | - John Ralph
- Department of Biochemistry, and The Department of Energy's Great Lakes Bioenergy Research Center, The Wisconsin Energy Institute , University of Wisconsin , Madison , Wisconsin 53726 , United States
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22
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Whiten SR, Ray WK, Helm RF, Adelman ZN. Characterization of the adult Aedes aegypti early midgut peritrophic matrix proteome using LC-MS. PLoS One 2018; 13:e0194734. [PMID: 29570734 PMCID: PMC5865745 DOI: 10.1371/journal.pone.0194734] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 03/08/2018] [Indexed: 02/01/2023] Open
Abstract
The Aedes aegypti mosquito is the principal vector of arboviruses such as dengue, chikungunya, yellow fever, and Zika virus. These arboviruses are transmitted during adult female mosquito bloodfeeding. While these viruses must transverse the midgut to replicate, the blood meal must also reach the midgut to be digested, absorbed, or excreted, as aggregation of blood meal metabolites can be toxic to the female mosquito midgut. The midgut peritrophic matrix (PM), a semipermeable extracellular layer comprised of chitin fibrils, glycoproteins, and proteoglycans, is one such mechanism of protection for the mosquito midgut. However, this structure has not been characterized for adult female Ae. aegypti. We conducted a mass spectrometry based proteomic analysis to identify proteins that comprise or are associated with the adult female Ae. aegypti early midgut PM. Altogether, 474 unique proteins were identified, with 115 predicted as secreted. GO-term enrichment analysis revealed an abundance of serine-type proteases and several known and novel intestinal mucins. In addition, approximately 10% of the peptides identified corresponded to known salivary proteins, indicating Ae. aegypti mosquitoes extensively swallow their own salivary secretions. However, the physiological relevance of this remains unclear, and further studies are needed to determine PM proteins integral for midgut protection from blood meal derived toxicity and pathogen protection. Finally, we describe substantial discordance between previously described transcriptionally changes observed in the midgut in response to a bloodmeal and the presence of the corresponding protein in the PM. Data are available via ProteomeXchange with identifier PXD007627.
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Affiliation(s)
- Shavonn R. Whiten
- Department of Entomology, Texas A&M University, College Station, Texas, United States of America
| | - W. Keith Ray
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Richard F. Helm
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Zach N. Adelman
- Department of Entomology, Texas A&M University, College Station, Texas, United States of America
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Shi H, Munk A, Nielsen TS, Daughtry MR, Larsson L, Li S, Høyer KF, Geisler HW, Sulek K, Kjøbsted R, Fisher T, Andersen MM, Shen Z, Hansen UK, England EM, Cheng Z, Højlund K, Wojtaszewski JFP, Yang X, Hulver MW, Helm RF, Treebak JT, Gerrard DE. Skeletal muscle O-GlcNAc transferase is important for muscle energy homeostasis and whole-body insulin sensitivity. Mol Metab 2018. [PMID: 29525407 PMCID: PMC6001359 DOI: 10.1016/j.molmet.2018.02.010] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Objective Given that cellular O-GlcNAcylation levels are thought to be real-time measures of cellular nutrient status and dysregulated O-GlcNAc signaling is associated with insulin resistance, we evaluated the role of O-GlcNAc transferase (OGT), the enzyme that mediates O-GlcNAcylation, in skeletal muscle. Methods We assessed O-GlcNAcylation levels in skeletal muscle from obese, type 2 diabetic people, and we characterized muscle-specific OGT knockout (mKO) mice in metabolic cages and measured energy expenditure and substrate utilization pattern using indirect calorimetry. Whole body insulin sensitivity was assessed using the hyperinsulinemic euglycemic clamp technique and tissue-specific glucose uptake was subsequently evaluated. Tissues were used for histology, qPCR, Western blot, co-immunoprecipitation, and chromatin immunoprecipitation analyses. Results We found elevated levels of O-GlcNAc-modified proteins in obese, type 2 diabetic people compared with well-matched obese and lean controls. Muscle-specific OGT knockout mice were lean, and whole body energy expenditure and insulin sensitivity were increased in these mice, consistent with enhanced glucose uptake and elevated glycolytic enzyme activities in skeletal muscle. Moreover, enhanced glucose uptake was also observed in white adipose tissue that was browner than that of WT mice. Interestingly, mKO mice had elevated mRNA levels of Il15 in skeletal muscle and increased circulating IL-15 levels. We found that OGT in muscle mediates transcriptional repression of Il15 by O-GlcNAcylating Enhancer of Zeste Homolog 2 (EZH2). Conclusions Elevated muscle O-GlcNAc levels paralleled insulin resistance and type 2 diabetes in humans. Moreover, OGT-mediated signaling is necessary for proper skeletal muscle metabolism and whole-body energy homeostasis, and our data highlight O-GlcNAcylation as a potential target for ameliorating metabolic disorders. Type 2 diabetic humans have elevated O-GlcNAc levels in skeletal muscle. Knockout of OGT in muscle elevates whole body insulin sensitivity. Knockout of OGT in muscle increases resistance to diet-induced obesity. Muscle-specific OGT knockout mice have elevated plasma IL-15 levels. OGT in muscle controls Il15 expression by O-GlcNAcylation and inhibition of EZH2.
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Affiliation(s)
- Hao Shi
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Alexander Munk
- Section of Integrative Physiology, Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, DK2200, Denmark
| | - Thomas S Nielsen
- Section of Integrative Physiology, Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, DK2200, Denmark
| | - Morgan R Daughtry
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Louise Larsson
- Section of Integrative Physiology, Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, DK2200, Denmark
| | - Shize Li
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Kasper F Høyer
- Section of Integrative Physiology, Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, DK2200, Denmark; Department of Endocrinology and Internal Medicine, Aarhus University Hospital, Aarhus, DK8000, Denmark
| | - Hannah W Geisler
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Karolina Sulek
- Section of Integrative Physiology, Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, DK2200, Denmark
| | - Rasmus Kjøbsted
- Section of Molecular Physiology, Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Copenhagen, DK2100, Denmark
| | - Taylor Fisher
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Marianne M Andersen
- Section of Integrative Physiology, Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, DK2200, Denmark
| | - Zhengxing Shen
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Ulrik K Hansen
- Section of Integrative Physiology, Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, DK2200, Denmark
| | - Eric M England
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Zhiyong Cheng
- Department of Human Nutrition, Foods, and Exercise, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Kurt Højlund
- Department of Endocrinology, Odense University Hospital, Odense, Denmark; Section of Molecular Diabetes and Metabolism, Institute of Molecular Medicine and Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Jørgen F P Wojtaszewski
- Section of Molecular Physiology, Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Copenhagen, DK2100, Denmark
| | - Xiaoyong Yang
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Matthew W Hulver
- Department of Human Nutrition, Foods, and Exercise, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA; The Virginia Tech Metabolic Phenotyping Core, Blacksburg, VA 24061, USA
| | - Richard F Helm
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Jonas T Treebak
- Section of Integrative Physiology, Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, DK2200, Denmark.
| | - David E Gerrard
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.
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24
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Vu LT, Orbach SM, Ray WK, Cassin ME, Rajagopalan P, Helm RF. The hepatocyte proteome in organotypic rat liver models and the influence of the local microenvironment. Proteome Sci 2017; 15:12. [PMID: 28649179 PMCID: PMC5480101 DOI: 10.1186/s12953-017-0120-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 06/15/2017] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Liver models that closely mimic the in vivo microenvironment are useful for understanding liver functions, capabilities, and intercellular communication processes. Three-dimensional (3D) liver models assembled using hepatocytes and liver sinusoidal endothelial cells (LSECs) separated by a polyelectrolyte multilayer (PEM) provide a functional system while also permitting isolation of individual cell types for proteomic analyses. METHODS To better understand the mechanisms and processes that underlie liver model function, hepatocytes were maintained as monolayers and 3D PEM-based formats in the presence or absence of primary LSECs. The resulting hepatocyte proteomes, the proteins in the PEM, and extracellular levels of urea, albumin and glucose after three days of culture were compared. RESULTS All systems were ketogenic and found to release glucose. The presence of the PEM led to increases in proteins associated with both mitochondrial and peroxisomal-based β-oxidation. The PEMs also limited production of structural and migratory proteins associated with dedifferentiation. The presence of LSECs increased levels of Phase I and Phase II biotransformation enzymes as well as several proteins associated with the endoplasmic reticulum and extracellular matrix remodeling. The proteomic analysis of the PEMs indicated that there was no significant change after three days of culture. These results are discussed in relation to liver model function. CONCLUSIONS Heterotypic cell-cell and cell-ECM interactions exert different effects on hepatocyte functions and phenotypes.
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Affiliation(s)
- Lucas T. Vu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061 USA
| | - Sophia M. Orbach
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061 USA
| | - W. Keith Ray
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061 USA
| | - Margaret E. Cassin
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061 USA
| | - Padmavathy Rajagopalan
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061 USA
- School of Biomedical Engineering and Sciences, Virginia Tech, Blacksburg, Virginia 24061 USA
- ICTAS Center for Systems Biology and Engineered Tissues, Virginia Tech, Blacksburg, Virginia 24061 USA
| | - Richard F. Helm
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061 USA
- ICTAS Center for Systems Biology and Engineered Tissues, Virginia Tech, Blacksburg, Virginia 24061 USA
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25
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Rothschild DE, Zhang Y, Diao N, Lee CK, Chen K, Caswell CC, Slade DJ, Helm RF, LeRoith T, Li L, Allen IC. Functional characterization of Irakm
rΔ9–11 splice variant in mice. The Journal of Immunology 2017. [DOI: 10.4049/jimmunol.198.supp.222.15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Ulcerative colitis (UC) and Crohn’s disease (CD) are two pathologies collectively referred to as Inflammatory Bowel Disease (IBD). While a definitive etiology is currently unknown, a complex interplay of environmental factors and genetic predispositions has been linked to IBD development. The Toll-like receptors (TLRs) are a family of pattern recognition receptors (PPRs) involved in the signaling pathways that regulate the inflammatory response, and as such, represent essential targets for therapeutic intervention of UC and CD. Interleukin receptor associated kinase M (IRAKM) is an important negative regulator of TLR signaling acting to attenuate an overzealous innate immune response. Metadata analysis of human patient samples afflicted with IBD revealed increased expression of IRAKM compared to both healthy controls and patients with inactive forms of IBD. Furthermore, our findings in murine studies have identified that commercially available Irakm−/− mice contain a spliced mRNA variant of the Irakm gene as a result of the knockout strategy; defined here to be IrakmrΔ9–11. We have found that the truncated IrakmrΔ9–11 protein robustly activates a NF-κB dependent luciferase reporter when overexpressed in mammalian cells. These results, together with data supporting the mechanistic role of this truncated protein, suggest an alternative explanation for the function of IRAK-M in TLR signaling and in modulating gastrointestinal immune homeostasis with potential therapeutic implications for IBD patients.
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Affiliation(s)
- Daniel E Rothschild
- 1Virginia-Maryland College of Veterinary Medicine
- 2Virginia Polytechnic Inst. and State Univ
| | - Yao Zhang
- 2Virginia Polytechnic Inst. and State Univ
| | - Na Diao
- 2Virginia Polytechnic Inst. and State Univ
| | | | | | - Clayton C Caswell
- 1Virginia-Maryland College of Veterinary Medicine
- 2Virginia Polytechnic Inst. and State Univ
| | | | | | - Tanya LeRoith
- 1Virginia-Maryland College of Veterinary Medicine
- 2Virginia Polytechnic Inst. and State Univ
| | - Liwu Li
- 2Virginia Polytechnic Inst. and State Univ
| | - Irving C Allen
- 1Virginia-Maryland College of Veterinary Medicine
- 2Virginia Polytechnic Inst. and State Univ
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Rothschild DE, Zhang Y, Diao N, Lee CK, Chen K, Caswell CC, Slade DJ, Helm RF, LeRoith T, Li L, Allen IC. Enhanced Mucosal Defense and Reduced Tumor Burden in Mice with the Compromised Negative Regulator IRAK-M. EBioMedicine 2016; 15:36-47. [PMID: 27939424 PMCID: PMC5233813 DOI: 10.1016/j.ebiom.2016.11.039] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 11/30/2016] [Accepted: 11/30/2016] [Indexed: 12/27/2022] Open
Abstract
Aberrant inflammation is a hallmark of inflammatory bowel disease (IBD) and colorectal cancer. IRAK-M is a critical negative regulator of TLR signaling and overzealous inflammation. Here we utilize data from human studies and Irak-m-/- mice to elucidate the role of IRAK-M in the modulation of gastrointestinal immune system homeostasis. In human patients, IRAK-M expression is up-regulated during IBD and colorectal cancer. Further functional studies in mice revealed that Irak-m-/- animals are protected against colitis and colitis associated tumorigenesis. Mechanistically, our data revealed that the gastrointestinal immune system of Irak-m-/- mice is highly efficient at eliminating microbial translocation following epithelial barrier damage. This attenuation of pathogenesis is associated with expanded areas of gastrointestinal associated lymphoid tissue (GALT), increased neutrophil migration, and enhanced T-cell recruitment. Further evaluation of Irak-m-/- mice revealed a splice variant that robustly activates NF-κB signaling. Together, these data identify IRAK-M as a potential target for future therapeutic intervention.
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Affiliation(s)
- Daniel E Rothschild
- Department of Biomedical Sciences and Pathobiology, VA-MD College of Veterinary Medicine, Blacksburg, Virginia 24061, United States
| | - Yao Zhang
- Department of Biological Sciences, Virginia Polytechnic and State University, Blacksburg, Virginia 24061, United States
| | - Na Diao
- Department of Biological Sciences, Virginia Polytechnic and State University, Blacksburg, Virginia 24061, United States
| | - Christina K Lee
- Department of Biological Sciences, Virginia Polytechnic and State University, Blacksburg, Virginia 24061, United States
| | - Keqiang Chen
- Department of Biological Sciences, Virginia Polytechnic and State University, Blacksburg, Virginia 24061, United States
| | - Clayton C Caswell
- Department of Biomedical Sciences and Pathobiology, VA-MD College of Veterinary Medicine, Blacksburg, Virginia 24061, United States
| | - Daniel J Slade
- Department of Biochemistry, Virginia Polytechnic and State University, Blacksburg, Virginia 24061, United States
| | - Richard F Helm
- Department of Biochemistry, Virginia Polytechnic and State University, Blacksburg, Virginia 24061, United States
| | - Tanya LeRoith
- Department of Biomedical Sciences and Pathobiology, VA-MD College of Veterinary Medicine, Blacksburg, Virginia 24061, United States
| | - Liwu Li
- Department of Biological Sciences, Virginia Polytechnic and State University, Blacksburg, Virginia 24061, United States.
| | - Irving C Allen
- Department of Biomedical Sciences and Pathobiology, VA-MD College of Veterinary Medicine, Blacksburg, Virginia 24061, United States.
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Webb BA, Karl Compton K, Castañeda Saldaña R, Arapov TD, Keith Ray W, Helm RF, Scharf BE. Sinorhizobium meliloti chemotaxis to quaternary ammonium compounds is mediated by the chemoreceptor McpX. Mol Microbiol 2016; 103:333-346. [PMID: 27748981 DOI: 10.1111/mmi.13561] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/13/2016] [Indexed: 12/27/2022]
Abstract
The bacterium Sinorhizobium meliloti is attracted to seed exudates of its host plant alfalfa (Medicago sativa). Since quaternary ammonium compounds (QACs) are exuded by germinating seeds, we assayed chemotaxis of S. meliloti towards betonicine, choline, glycine betaine, stachydrine and trigonelline. The wild type displayed a positive response to all QACs. Using LC-MS, we determined that each germinating alfalfa seed exuded QACs in the nanogram range. Compared to the closely related nonhost species, spotted medic (Medicago arabica), unique profiles were released. Further assessments of single chemoreceptor deletion strains revealed that an mcpX deletion strain displayed little to no response to these compounds. Differential scanning fluorimetry showed interaction of the isolated periplasmic region of McpX (McpXPR and McpX34-306 ) with QACs. Isothermal titration calorimetry experiments revealed tight binding to McpXPR with dissociation constants (Kd ) in the nanomolar range for choline and glycine betaine, micromolar Kd for stachydrine and trigonelline and a Kd in the millimolar range for betonicine. Our discovery of S. meliloti chemotaxis to plant-derived QACs adds another role to this group of compounds, which are known to serve as nutrient sources, osmoprotectants and cell-to-cell signalling molecules. This is the first report of a chemoreceptor that mediates QACs taxis through direct binding.
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Affiliation(s)
- Benjamin A Webb
- Department of Biological Sciences, Life Sciences I, Virginia Tech, Blacksburg, VA, 24061, USA
| | - K Karl Compton
- Department of Biological Sciences, Life Sciences I, Virginia Tech, Blacksburg, VA, 24061, USA
| | | | - Timofey D Arapov
- Department of Biological Sciences, Life Sciences I, Virginia Tech, Blacksburg, VA, 24061, USA
| | - W Keith Ray
- Department of Biochemistry, Life Sciences I, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Richard F Helm
- Department of Biochemistry, Life Sciences I, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Birgit E Scharf
- Department of Biological Sciences, Life Sciences I, Virginia Tech, Blacksburg, VA, 24061, USA
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Berardi AE, Hildreth SB, Helm RF, Winkel BSJ, Smith SD. Evolutionary correlations in flavonoid production across flowers and leaves in the Iochrominae (Solanaceae). Phytochemistry 2016; 130:119-27. [PMID: 27291343 DOI: 10.1016/j.phytochem.2016.05.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 05/12/2016] [Accepted: 05/23/2016] [Indexed: 05/21/2023]
Abstract
Plant reproductive and vegetative tissues often use the same biochemical pathways to produce specialized metabolites. In such cases, selection acting on the synthesis of specific products in a particular tissue could result in correlated changes in other products of the pathway, both in the same tissue and in other tissues. This study examined how changes in floral anthocyanin pigmentation affect the production of other compounds of the flavonoid pathway in flowers and in leaves. Focusing on the Iochrominae, a clade of Solanaceae with a wide range of flower colors, liquid chromatography coupled with mass spectrometry and UV detection was used to profile and quantify the variation in two classes of flavonoids, anthocyanins and flavonols. Purple, red, orange and white-flowered Iochrominae produced all of the six common anthocyanidin types, as well as several classes of flavonols. Differences in anthocyanin and flavonol production were significantly correlated in flowers, particularly with respect to B ring hydroxylation pattern. However, these differences in floral flavonoids were not strongly related to differences in leaf chemistry. Specifically, most species made only flavonols (not anthocyanins) in leaves, and these comprised the two most common flavonols, quercetin and kaempferol, regardless of the color of the flower. These results suggest that shifts in flower color may occur without significant pleiotropic consequences for flavonoid production in vegetative tissues. Similar studies in other systems will be important for testing the generality of this pattern in other groups of flowering plants.
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Affiliation(s)
- Andrea E Berardi
- Department of Ecology and Evolutionary Biology, University of Colorado-Boulder, Campus Box 334, Boulder, CO, 80309, USA.
| | - Sherry B Hildreth
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Richard F Helm
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Brenda S J Winkel
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Stacey D Smith
- Department of Ecology and Evolutionary Biology, University of Colorado-Boulder, Campus Box 334, Boulder, CO, 80309, USA
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Velander P, Wu L, Ray WK, Helm RF, Xu B. Amylin Amyloid Inhibition by Flavonoid Baicalein: Key Roles of Its Vicinal Dihydroxyl Groups of the Catechol Moiety. Biochemistry 2016; 55:4255-8. [DOI: 10.1021/acs.biochem.6b00578] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Paul Velander
- Department of Biochemistry, ‡Center for Drug Discovery, and §Translational Obesity Research Center, Virginia Polytechnic Institute & State University, Blacksburg, Virginia 24061, United States
| | - Ling Wu
- Department of Biochemistry, ‡Center for Drug Discovery, and §Translational Obesity Research Center, Virginia Polytechnic Institute & State University, Blacksburg, Virginia 24061, United States
| | - W. Keith Ray
- Department of Biochemistry, ‡Center for Drug Discovery, and §Translational Obesity Research Center, Virginia Polytechnic Institute & State University, Blacksburg, Virginia 24061, United States
| | - Richard F. Helm
- Department of Biochemistry, ‡Center for Drug Discovery, and §Translational Obesity Research Center, Virginia Polytechnic Institute & State University, Blacksburg, Virginia 24061, United States
| | - Bin Xu
- Department of Biochemistry, ‡Center for Drug Discovery, and §Translational Obesity Research Center, Virginia Polytechnic Institute & State University, Blacksburg, Virginia 24061, United States
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Webb BA, Helm RF, Scharf BE. Contribution of Individual Chemoreceptors to Sinorhizobium meliloti Chemotaxis Towards Amino Acids of Host and Nonhost Seed Exudates. Mol Plant Microbe Interact 2016; 29:231-9. [PMID: 26713349 DOI: 10.1094/mpmi-12-15-0264-r] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Plant seeds and roots exude a spectrum of molecules into the soil that attract bacteria to the spermosphere and rhizosphere, respectively. The alfalfa symbiont Sinorhizobium meliloti utilizes eight chemoreceptors (McpT to McpZ and IcpA) to mediate chemotaxis. Using a modified hydrogel capillary chemotaxis assay that allows data quantification and larger throughput screening, we defined the role of S. meliloti chemoreceptors in sensing its host, Medicago sativa, and a closely related nonhost, Medicago arabica. S. meliloti wild type and most single-deletion strains displayed comparable chemotaxis responses to host or nonhost seed exudate. However, while the mcpZ mutant responded like wild type to M. sativa exudate, its reaction to M. arabica exudate was reduced by 80%. Even though the amino acid (AA) amounts released by both plant species were similar, synthetic AA mixtures that matched exudate profiles contributed differentially to the S. meliloti wild-type response to M. sativa (23%) and M. arabica (37%) exudates, with McpU identified as the most important chemoreceptor for AA. Our results show that S. meliloti is equally attracted to host and nonhost legumes; however, AA play a greater role in attraction to M. arabica than to M. sativa, with McpZ being specifically important in sensing M. arabica.
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Affiliation(s)
| | - Richard F Helm
- 2 Virginia Tech Department of Biochemistry, Life Sciences I, Blacksburg, VA 24061, U.S.A
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Redekar NR, Biyashev RM, Jensen RV, Helm RF, Grabau EA, Maroof MAS. Genome-wide transcriptome analyses of developing seeds from low and normal phytic acid soybean lines. BMC Genomics 2015; 16:1074. [PMID: 26678836 PMCID: PMC4683714 DOI: 10.1186/s12864-015-2283-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Accepted: 12/10/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Low phytic acid (lpa) crops are potentially eco-friendly alternative to conventional normal phytic acid (PA) crops, improving mineral bioavailability in monogastric animals as well as decreasing phosphate pollution. The lpa crops developed to date carry mutations that are directly or indirectly associated with PA biosynthesis and accumulation during seed development. These lpa crops typically exhibit altered carbohydrate profiles, increased free phosphate, and lower seedling emergence, the latter of which reduces overall crop yield, hence limiting their large-scale cultivation. Improving lpa crop yield requires an understanding of the downstream effects of the lpa genotype on seed development. Towards that end, we present a comprehensive comparison of gene-expression profiles between lpa and normal PA soybean lines (Glycine max) at five stages of seed development using RNA-Seq approaches. The lpa line used in this study carries single point mutations in a myo-inositol phosphate synthase gene along with two multidrug-resistance protein ABC transporter genes. RESULTS RNA sequencing data of lpa and normal PA soybean lines from five seed-developmental stages (total of 30 libraries) were used for differential expression and functional enrichment analyses. A total of 4235 differentially expressed genes, including 512-transcription factor genes were identified. Eighteen biological processes such as apoptosis, glucan metabolism, cellular transport, photosynthesis and 9 transcription factor families including WRKY, CAMTA3 and SNF2 were enriched during seed development. Genes associated with apoptosis, glucan metabolism, and cellular transport showed enhanced expression in early stages of lpa seed development, while those associated with photosynthesis showed decreased expression in late developmental stages. The results suggest that lpa-causing mutations play a role in inducing and suppressing plant defense responses during early and late stages of seed development, respectively. CONCLUSIONS This study provides a global perspective of transcriptomal changes during soybean seed development in an lpa mutant. The mutants are characterized by earlier expression of genes associated with cell wall biosynthesis and a decrease in photosynthetic genes in late stages. The biological processes and transcription factors identified in this study are signatures of lpa-causing mutations.
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Affiliation(s)
- Neelam R Redekar
- Department of Crop and Soil Environmental Sciences, Virginia Tech, 185 AgQuad Lane, 24061, Blacksburg, VA, USA.
| | - Ruslan M Biyashev
- Department of Crop and Soil Environmental Sciences, Virginia Tech, 185 AgQuad Lane, 24061, Blacksburg, VA, USA.
| | - Roderick V Jensen
- Department of Biological Sciences, Virginia Tech, Life Science I building, 24061, Blacksburg, VA, USA.
| | - Richard F Helm
- Department of Biochemistry, Virginia Tech, Life Science I building, 24061, Blacksburg, VA, USA.
| | - Elizabeth A Grabau
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Price Hall, 24061, Blacksburg, VA, USA.
| | - M A Saghai Maroof
- Department of Crop and Soil Environmental Sciences, Virginia Tech, 185 AgQuad Lane, 24061, Blacksburg, VA, USA.
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Jervis J, Kastl C, Hildreth SB, Biyashev R, Grabau EA, Saghai-Maroof MA, Helm RF. Metabolite Profiling of Soybean Seed Extracts from Near-Isogenic Low and Normal Phytate Lines Using Orthogonal Separation Strategies. J Agric Food Chem 2015; 63:9879-87. [PMID: 26487475 DOI: 10.1021/acs.jafc.5b04002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Untargeted metabolomic profiling using liquid chromatography-mass spectrometry (LC-MS) was applied to lipid-depleted methanolic extracts of soybean seeds utilizing orthogonal chromatographic separations (reversed-phase and hydrophilic interaction) in both positive and negative ionization modes. Four near-isogenic lines (NILs) differing in mutations for two genes encoding highly homologous multidrug resistant proteins (MRPs) were evaluated. The double mutant exhibited a low phytate phenotype, whereas the other three NILs, the two single mutants and the wild type, did not. Principal component analysis (PCA) of the four LC-MS data sets fully separated the low phytate line from the other three. While the levels of neutral oligosaccharides were the same for all lines, there were significant metabolite differences residing in the levels of malonyl isoflavones, soyasaponins, and arginine. Two methanol-soluble polypeptides were also found as differing in abundance levels, one of which was identified as the allergen Gly m 1.
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Affiliation(s)
- Judith Jervis
- Departments of Biochemistry, ‡Crop and Soil Environmental Sciences, §Biological Sciences, and Plant Pathology, and ∥Physiology and Weed Science, Virginia Tech , Blacksburg, Virginia 24061, United States
| | - Christin Kastl
- Departments of Biochemistry, ‡Crop and Soil Environmental Sciences, §Biological Sciences, and Plant Pathology, and ∥Physiology and Weed Science, Virginia Tech , Blacksburg, Virginia 24061, United States
| | - Sherry B Hildreth
- Departments of Biochemistry, ‡Crop and Soil Environmental Sciences, §Biological Sciences, and Plant Pathology, and ∥Physiology and Weed Science, Virginia Tech , Blacksburg, Virginia 24061, United States
| | - Ruslan Biyashev
- Departments of Biochemistry, ‡Crop and Soil Environmental Sciences, §Biological Sciences, and Plant Pathology, and ∥Physiology and Weed Science, Virginia Tech , Blacksburg, Virginia 24061, United States
| | - Elizabeth A Grabau
- Departments of Biochemistry, ‡Crop and Soil Environmental Sciences, §Biological Sciences, and Plant Pathology, and ∥Physiology and Weed Science, Virginia Tech , Blacksburg, Virginia 24061, United States
| | - Mohammad A Saghai-Maroof
- Departments of Biochemistry, ‡Crop and Soil Environmental Sciences, §Biological Sciences, and Plant Pathology, and ∥Physiology and Weed Science, Virginia Tech , Blacksburg, Virginia 24061, United States
| | - Richard F Helm
- Departments of Biochemistry, ‡Crop and Soil Environmental Sciences, §Biological Sciences, and Plant Pathology, and ∥Physiology and Weed Science, Virginia Tech , Blacksburg, Virginia 24061, United States
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33
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Ralph J, Helm RF. Lignin/Hydroxycinnamic Acid/Polysaccharide Complexes: Synthetic Models for Regiochemical Characterization. Forage Cell Wall Structure and Digestibility 2015. [DOI: 10.2134/1993.foragecellwall.c9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- John Ralph
- USDA-ARS, U.S. Dairy Forage Research Center; Madison Wisconsin
| | - Richard F. Helm
- USDA-ARS, U.S. Dairy Forage Research Center; Madison Wisconsin
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Jervis J, Hildreth SB, Sheng X, Beers EP, Brunner AM, Helm RF. A metabolomic assessment of NAC154 transcription factor overexpression in field grown poplar stem wood. Phytochemistry 2015; 115:112-20. [PMID: 25771508 DOI: 10.1016/j.phytochem.2015.02.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 12/19/2014] [Accepted: 02/08/2015] [Indexed: 05/24/2023]
Abstract
Several xylem-associated regulatory genes have been identified that control processes associated with wood formation in poplar. Prominent among these are the NAC domain transcription factors (NACs). Here, the putative involvement of Populus NAC154, a co-ortholog of the Arabidopsis gene SND2, was evaluated as a regulator of "secondary" biosynthetic processes in stem internode tissues by interrogating aqueous methanolic extracts from control and transgenic trees. Comprehensive untargeted metabolite profiling was accomplished with a liquid chromatography-mass spectrometry platform that utilized two different chromatographic supports (HILIC and reversed phase) and both positive and negative ionization modes. Evaluation of current and previous year tissues provided datasets for assessing the effects of NAC154 overexpression in wood maturation processes. Phenolic glycoside levels as well as those of oligolignols, sucrose and arginine were modulated with phenotypic and chemotypic traits exhibiting similar trends. Specifically, increased levels of arginine in the NAC154 overexpressing tissues supports a role for the transcription factor in senescence/dormancy-associated processes.
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Affiliation(s)
- Judith Jervis
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
| | - Sherry B Hildreth
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - Xiaoyan Sheng
- Department of Forest Resources and Environmental Conservation, Virginia Tech, Blacksburg, VA 24061, USA
| | - Eric P Beers
- Department of Horticulture, Virginia Tech, Blacksburg, VA 24061, USA
| | - Amy M Brunner
- Department of Forest Resources and Environmental Conservation, Virginia Tech, Blacksburg, VA 24061, USA
| | - Richard F Helm
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA.
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35
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Chen Y, Ray WK, Helm RF, Melville SB, Popham DL. Levels of germination proteins in Bacillus subtilis dormant, superdormant, and germinating spores. PLoS One 2014; 9:e95781. [PMID: 24752279 PMCID: PMC3994143 DOI: 10.1371/journal.pone.0095781] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 03/31/2014] [Indexed: 12/24/2022] Open
Abstract
Bacterial endospores exhibit extreme resistance to most conditions that rapidly kill other life forms, remaining viable in this dormant state for centuries or longer. While the majority of Bacillus subtilis dormant spores germinate rapidly in response to nutrient germinants, a small subpopulation termed superdormant spores are resistant to germination, potentially evading antibiotic and/or decontamination strategies. In an effort to better understand the underlying mechanisms of superdormancy, membrane-associated proteins were isolated from populations of B. subtilis dormant, superdormant, and germinated spores, and the relative abundance of 11 germination-related proteins was determined using multiple-reaction-monitoring liquid chromatography-mass spectrometry assays. GerAC, GerKC, and GerD were significantly less abundant in the membrane fractions obtained from superdormant spores than those derived from dormant spores. The amounts of YpeB, GerD, PrkC, GerAC, and GerKC recovered in membrane fractions decreased significantly during germination. Lipoproteins, as a protein class, decreased during spore germination, while YpeB appeared to be specifically degraded. Some protein abundance differences between membrane fractions of dormant and superdormant spores resemble protein changes that take place during germination, suggesting that the superdormant spore isolation procedure may have resulted in early, non-committal germination-associated changes. In addition to low levels of germinant receptor proteins, a deficiency in the GerD lipoprotein may contribute to heterogeneity of spore germination rates. Understanding the reasons for superdormancy may allow for better spore decontamination procedures.
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Affiliation(s)
- Yan Chen
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
| | - W. Keith Ray
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Richard F. Helm
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Stephen B. Melville
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
| | - David L. Popham
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
- * E-mail:
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Vilhauer L, Jervis J, Ray WK, Helm RF. The exo-proteome and exo-metabolome of Nostoc punctiforme (Cyanobacteria) in the presence and absence of nitrate. Arch Microbiol 2014; 196:357-67. [PMID: 24643449 DOI: 10.1007/s00203-014-0974-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 02/27/2014] [Indexed: 01/04/2023]
Abstract
The ability of nitrogen-fixing filamentous Cyanobacteria to adapt to multiple environments comes in part from assessing and responding to external stimuli, an event that is initiated in the extracellular milieu. While it is known that these organisms produce numerous extracellular substances, little work has been done to characterize both the metabolites and proteins present under standard laboratory growth conditions. We have assessed the extracellular milieu of Nostoc punctiforme when grown in liquid culture in the presence and absence of a nitrogen source (nitrate). The extracellular proteins identified were enriched in integrin β-propellor domains and calcium-binding sites with sequences unique to N. punctiforme, supporting a role for extracellular proteins in modulating species-specific recognition and behavior processes. Extracellular proteases are present and active under both conditions, with the cells grown with nitrate having a higher activity when normalized to chlorophyll levels. The released metabolites are enriched in peptidoglycan-derived tetrasaccharides, with higher levels in nitrate-free media.
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Affiliation(s)
- Laura Vilhauer
- Department of Biochemistry, Virginia Tech, 143 Life Sciences 1, Blacksburg, VA, 24061-0910, USA
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Slade WO, Ray WK, Williams PM, Winkel BSJ, Helm RF. Effects of exogenous auxin and ethylene on the Arabidopsis root proteome. Phytochemistry 2012; 84:18-23. [PMID: 22989740 DOI: 10.1016/j.phytochem.2012.08.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Revised: 07/19/2012] [Accepted: 08/13/2012] [Indexed: 06/01/2023]
Abstract
The phytohormones, auxin and ethylene, together control a wide range of physiological and developmental processes in plants. The lack of knowledge regarding how the underlying signaling processes are reflected at the protein level represents a major gap in understanding phytohormone signaling, including that mediated by crosstalk between auxin and ethylene. Herein is a parallel comparison of the effects of these two hormones on the Arabidopsis root proteome. Arabidopsis seedlings were exposed to 1 μm indole-3-acetic acid (IAA, auxin) or 1 μm 1-amino-cyclopropane carboxylic acid (ACC) for 24h. Root protein extracts were fractionated using two-dimensional gel electrophoresis and the proteins that changed the most were analyzed by MALDI TOF/TOF mass spectrometry. Of the 500 total spots that were matched across all gels, 24 were significantly different after IAA exposure, while seven others were different after ACC exposure. Using rigorous criteria, identities of eight proteins regulated by IAA and five regulated by ACC were assigned. Interestingly, although both hormones affected proteins associated with fundamental cellular processes, no overlap was observed among the proteins affected by auxin or ethylene treatment. This report provides a comparison of the effects of these two hormones relative to a control utilizing equivalent treatment regimes and suggests that, while these hormones communicate to control similar physiological and transcriptional processes, they have different effects on the most abundant proteins in Arabidopsis roots.
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Affiliation(s)
- William O Slade
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061-0406, USA
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Potts M, Slaughter SM, Hunneke FU, Garst JF, Helm RF. Desiccation tolerance of prokaryotes: application of principles to human cells. Integr Comp Biol 2012; 45:800-9. [PMID: 21676831 DOI: 10.1093/icb/45.5.800] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The loss of water from cells is a stress that was likely imposed very early in evolution. An understanding of the sensitivity or tolerance of cells to depletion of intracellular water is relevant to the study of quiescence, longevity and aging, because one consequence of air-drying is full metabolic arrest, sometimes for extended periods. When considering the adaptation of cells to physiological extremes of pH, temperature or pressure, it is generally assumed that evolution is driven toward optimum function rather than maximum stability. However, adaptation to desiccation has the singular and crucial distinction that dried cells do not grow, and the time the cell is dried may represent the greater part of the life (the time the cell remains viable) of that cell and its component macromolecules. Is a consideration of "function" relevant in the context of desiccated cells? The response of prokaryotic cells to desiccation, and the mechanisms they employ to tolerate this stress at the level of the cell, genome and proteome are considered. Fundamental principles were then implemented in the design of strategies to achieve air-dry stabilization of sensitive eukaryotic (human) cells. The responses of the transcriptomes and proteomes of prokaryotic cells and eukaryotic cells (yeast and human) to drying in air are compared and contrasted to achieve an evolutionary context. The concept of the "desiccome" is developed to question whether there is common set of structural, physiological and molecular mechanisms that constitute desiccation tolerance.
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Affiliation(s)
- Malcolm Potts
- Virginia Tech Center for Genomics, Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061
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Bowerman PA, Ramirez MV, Price MB, Helm RF, Winkel BSJ. Analysis of T-DNA alleles of flavonoid biosynthesis genes in Arabidopsis ecotype Columbia. BMC Res Notes 2012; 5:485. [PMID: 22947320 PMCID: PMC3526476 DOI: 10.1186/1756-0500-5-485] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 08/23/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The flavonoid pathway is a long-standing and important tool for plant genetics, biochemistry, and molecular biology. Numerous flavonoid mutants have been identified in Arabidopsis over the past several decades in a variety of ecotypes. Here we present an analysis of Arabidopsis lines of ecotype Columbia carrying T-DNA insertions in genes encoding enzymes of the central flavonoid pathway. We also provide a comprehensive summary of various mutant alleles for these structural genes that have been described in the literature to date in a wide variety of ecotypes. FINDINGS The confirmed knockout lines present easily-scorable phenotypes due to altered pigmentation of the seed coat (or testa). Knockouts for seven alleles for six flavonoid biosynthetic genes were confirmed by PCR and characterized by UPLC for altered flavonol content. CONCLUSION Seven mutant lines for six genes of the central flavonoid pathway were characterized in ecotype, Columbia. These lines represent a useful resource for integrating biochemical and physiological studies with genomic, transcriptomic, and proteomic data, much of which has been, and continues to be, generated in the Columbia background.
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Vallabhaneni P, Keith Ray W, Winkel BSJ, Helm RF. Characterization of flavonol glycosides in individual Arabidopsis root tips by flow injection electrospray mass spectrometry. Phytochemistry 2012; 73:114-118. [PMID: 22074608 DOI: 10.1016/j.phytochem.2011.09.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Revised: 09/16/2011] [Accepted: 09/28/2011] [Indexed: 05/31/2023]
Abstract
Developments in mass spectrometry-based technologies are offering insights into the complexity and dynamic nature of plant metabolism. However, the ability to generate reliable metabolic profiles at high spatial resolution is still limited by the need of most technologies for large sample sizes or time-intensive extraction and detection methods. Here we describe the use of flow injection electrospray mass spectrometry for the rapid identification and semi-quantitative analysis of flavonol glycosides in individual root tips. This method uncovered spatial and temporal differences in metabolic profiles that were masked in analyses of whole roots or seedlings, while showing that individual biological replicates can be extremely consistent.
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Lewis DR, Ramirez MV, Miller ND, Vallabhaneni P, Ray WK, Helm RF, Winkel BS, Muday GK. Auxin and ethylene induce flavonol accumulation through distinct transcriptional networks. Plant Physiol 2011; 156:144-64. [PMID: 21427279 PMCID: PMC3091047 DOI: 10.1104/pp.111.172502] [Citation(s) in RCA: 187] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Accepted: 03/19/2011] [Indexed: 05/18/2023]
Abstract
Auxin and ethylene are key regulators of plant growth and development, and thus the transcriptional networks that mediate responses to these hormones have been the subject of intense research. This study dissected the hormonal cross talk regulating the synthesis of flavonols and examined their impact on root growth and development. We analyzed the effects of auxin and an ethylene precursor on roots of wild-type and hormone-insensitive Arabidopsis (Arabidopsis thaliana) mutants at the transcript, protein, and metabolite levels at high spatial and temporal resolution. Indole-3-acetic acid (IAA) and 1-aminocyclopropane-1-carboxylic acid (ACC) differentially increased flavonol pathway transcripts and flavonol accumulation, altering the relative abundance of quercetin and kaempferol. The IAA, but not ACC, response is lost in the transport inhibitor response1 (tir1) auxin receptor mutant, while ACC responses, but not IAA responses, are lost in ethylene insensitive2 (ein2) and ethylene resistant1 (etr1) ethylene signaling mutants. A kinetic analysis identified increases in transcripts encoding the transcriptional regulators MYB12, Transparent Testa Glabra1, and Production of Anthocyanin Pigment after hormone treatments, which preceded increases in transcripts encoding flavonoid biosynthetic enzymes. In addition, myb12 mutants were insensitive to the effects of auxin and ethylene on flavonol metabolism. The equivalent phenotypes for transparent testa4 (tt4), which makes no flavonols, and tt7, which makes kaempferol but not quercetin, showed that quercetin derivatives are the inhibitors of basipetal root auxin transport, gravitropism, and elongation growth. Collectively, these experiments demonstrate that auxin and ethylene regulate flavonol biosynthesis through distinct signaling networks involving TIR1 and EIN2/ETR1, respectively, both of which converge on MYB12. This study also provides new evidence that quercetin is the flavonol that modulates basipetal auxin transport.
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Helm RF, Jervis J, Ray WK, Willoughby N, Irvin B, Hastie J, Schell DJ, Nagle N. Mass spectral analyses of corn stover prehydrolysates to assess conditioning processes. J Agric Food Chem 2010; 58:12642-12649. [PMID: 21080713 DOI: 10.1021/jf1031197] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Flow injection electrospray (FIE) and LC-tandem mass spectrometry techniques were used to characterize corn stover acid hydrolysates before and after overliming and ammonia conditioning steps. Analyses were performed on samples without fractionation (dilution only) in an effort provide an inventory of ionizable substances. Statistical evaluation of the results indicates that the ammonia-treated and crude hydrolysates were more similar to one another than any other pairing, with conditioning leading to a decrease in malate levels. LC-tandem mass spectrometry studies were also developed to characterize the oligosaccharides present in each hydrolysate utilizing a hydrophilic interaction chromatographic separation method. Neutral and acidic pentose-based oligosaccharides (xylodextrins) with degrees of polymerization between 2 and 5 were quantified with 4-O-methyl glucuronic acid-containing dimer and trimers predominating. Conditioning had little effect on the quantified oligosaccharide pool.
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Affiliation(s)
- Richard F Helm
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061-0910, United States.
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Oppenheimer M, Poulin MB, Lowary TL, Helm RF, Sobrado P. Characterization of recombinant UDP-galactopyranose mutase from Aspergillus fumigatus. Arch Biochem Biophys 2010; 502:31-8. [PMID: 20615386 DOI: 10.1016/j.abb.2010.06.035] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2010] [Revised: 06/29/2010] [Accepted: 06/29/2010] [Indexed: 11/26/2022]
Abstract
UDP-galactopyranose mutase (UGM) is a flavin-containing enzyme that catalyzes the conversion of UDP-galactopyranose to UDP-galactofuranose, the precursor of galactofuranose, which is an important cell wall component in Aspergillus fumigatus and other pathogenic microbes. A. fumigatus UGM (AfUGM) was expressed in Escherichia coli and purified to homogeneity. The enzyme was shown to function as a homotetramer by size-exclusion chromatography and to contain approximately 50% of the flavin in the active reduced form. A k(cat) value of 72 +/- 4 s(-1) and a K(M) value of 110 +/- 15 microM were determined with UDP-galactofuranose as substrate. In the oxidized state, AfUGM does not bind UDP-galactopyranose, while UDP and UDP-glucose bind with K(d) values of 33 +/- 9 microM and 90 +/- 30 microM, respectively. Functional and structural differences between the bacterial and eukaryotic UGMs are discussed.
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Oppenheimer ML, Blumer A, Poulin MB, Helm RF, Lowary TL, Sobrado P. Mechanistic studies on UDP‐Galactopyranose mutases from Aspergillus fumigatus and Trypanosoma cruzi. FASEB J 2010. [DOI: 10.1096/fasebj.24.1_supplement.513.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Oppenheimer M, Pierce BS, Crawford JA, Ray K, Helm RF, Sobrado P. Recombinant expression, purification, and characterization of ThmD, the oxidoreductase component of tetrahydrofuran monooxygenase. Arch Biochem Biophys 2010; 496:123-31. [PMID: 20159007 DOI: 10.1016/j.abb.2010.02.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Revised: 02/09/2010] [Accepted: 02/10/2010] [Indexed: 11/29/2022]
Abstract
Tetrahydrofuran monooxygenase (Thm) catalyzes the NADH-and oxygen-dependent hydroxylation of tetrahydrofuran to 2-hydroxytetrahydrofuran. Thm is composed of a hydroxylase enzyme, a regulatory subunit, and an oxidoreductase named ThmD. ThmD was expressed in Escherichia coli as a fusion to maltose-binding protein (MBP) and isolated to homogeneity after removal of the MBP. Purified ThmD contains covalently bound FAD, [2Fe-2S] center, and was shown to use ferricyanide, cytochrome c, 2,6-dichloroindophenol, and to a lesser extent, oxygen as surrogate electron acceptors. ThmD displays 160-fold preference for NADH over NADPH and functions as a monomer. The flavin-binding domain of ThmD (ThmD-FD) was purified and characterized. ThmD-FD displayed similar activity as the full-length ThmD and showed a unique flavin spectrum with a major peak at 463nm and a small peak at 396 nm. Computational modeling and mutagenesis analyses suggest a novel three-dimensional fold or covalent flavin attachment in ThmD.
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Barnoy S, Jeong KI, Helm RF, Suvarnapunya AE, Ranallo RT, Tzipori S, Venkatesan MM. Characterization of WRSs2 and WRSs3, new second-generation virG(icsA)-based Shigella sonnei vaccine candidates with the potential for reduced reactogenicity. Vaccine 2009; 28:1642-54. [PMID: 19932216 DOI: 10.1016/j.vaccine.2009.11.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2009] [Revised: 09/02/2009] [Accepted: 11/03/2009] [Indexed: 11/28/2022]
Abstract
Live, attenuated Shigella vaccine candidates, such as Shigella sonnei strain WRSS1, Shigella flexneri 2a strain SC602, and Shigella dysenteriae 1 strain WRSd1, are attenuated principally by the loss of the VirG(IcsA) protein. These candidates have proven to be safe and immunogenic in volunteer trials and in one study, efficacious against shigellosis. One drawback of these candidate vaccines has been the reactogenic symptoms of fever and diarrhea experienced by the volunteers, that increased in a dose-dependent manner. New, second-generation virG(icsA)-based S. sonnei vaccine candidates, WRSs2 and WRSs3, are expected to be less reactogenic while retaining the ability to generate protective levels of immunogenicity seen with WRSS1. Besides the loss of VirG(IcsA), WRSs2 and WRSs3 also lack plasmid-encoded enterotoxin ShET2-1 and its paralog ShET2-2. WRSs3 further lacks MsbB2 that reduces the endotoxicity of the lipid A portion of the bacterial LPS. Studies in cell cultures and in gnotobiotic piglets demonstrate that WRSs2 and WRSs3 have the potential to cause less diarrhea due to loss of ShET2-1 and ShET2-2 as well as alleviate febrile symptoms by loss of MsbB2. In guinea pigs, WRSs2 and WRSs3 were as safe, immunogenic and efficacious as WRSS1.
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Affiliation(s)
- S Barnoy
- Division of Bacterial & Rickettsial Diseases, Walter Reed Army Institute of Research 503, Robert Grant Avenue, Silver Spring, MD 208914, United States
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Tadepalli S, Ramakrishnan N, Watson LT, Mishra B, Helm RF. Simultaneously segmenting multiple gene expression time courses by analyzing cluster dynamics. J Bioinform Comput Biol 2009; 7:339-56. [PMID: 19340919 DOI: 10.1142/s0219720009004114] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2008] [Revised: 11/18/2008] [Accepted: 12/16/2008] [Indexed: 11/18/2022]
Abstract
We present a new approach to segmenting multiple time series by analyzing the dynamics of cluster formation and rearrangement around putative segment boundaries. This approach finds application in distilling large numbers of gene expression profiles into temporal relationships underlying biological processes. By directly minimizing information-theoretic measures of segmentation quality derived from Kullback-Leibler (KL) divergences, our formulation reveals clusters of genes along with a segmentation such that clusters show concerted behavior within segments but exhibit significant regrouping across segmentation boundaries. The results of the segmentation algorithm can be summarized as Gantt charts revealing temporal dependencies in the ordering of key biological processes. Applications to the yeast metabolic cycle and the yeast cell cycle are described.
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Affiliation(s)
- Satish Tadepalli
- Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.
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Sweede M, Ankem G, Chutvirasakul B, Azurmendi HF, Chbeir S, Watkins J, Helm RF, Finkielstein CV, Capelluto DGS. Structural and membrane binding properties of the prickle PET domain. Biochemistry 2009; 47:13524-36. [PMID: 19053268 DOI: 10.1021/bi801037h] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The planar cell polarity (PCP) pathway is required for fetal tissue morphogenesis as well as for maintenance of adult tissues in animals as diverse as fruit flies and mice. One of the key members of this pathway is Prickle (Pk), a protein that regulates cell movement through its association with the Dishevelled (Dsh) protein. Pk presents three LIM domains and a PET domain of unknown structure and function. Both the PET and LIM domains control membrane targeting of Dsh, which is necessary for Dsh function in the PCP pathway. Here, we show that the PET domain is monomeric and presents a nonglobular conformation with some properties of intrinsically disordered proteins. The PET domain adopts a helical conformation in the presence of 2,2,2-trifluoroethanol (TFE), a solvent known to stabilize hydrogen bonds within the polypeptide backbone, as analyzed by circular dichroism (CD) and NMR spectroscopy. Furthermore, we found that the conserved and single tryptophan residue in PET, Trp 536, moves to a more hydrophobic environment when accompanied with membrane penetration and that the protein becomes more helical in the presence of lipid micelles. The presence of LIM domains, downstream of PET, increases protein folding, thermostability, and tolerance to limited proteolysis. In addition, pull-down and tryptophan fluorescence analyses suggest that the LIM domains physically interact to regulate membrane penetration of the PET domain. The findings reported here favor a model where the PET domain is engaged in Pk membrane insertion, whereas the LIM domains modulate this function.
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Affiliation(s)
- Matthew Sweede
- Department of Chemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
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Park C, Helm RF, Novak JT. Investigating the fate of activated sludge extracellular proteins in sludge digestion using sodium dodecyl sulfate polyacrylamide gel electrophoresis. Water Environ Res 2008; 80:2219-2227. [PMID: 19146099 DOI: 10.2175/106143008x325791] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The fate of activated sludge extracellular proteins in sludge digestion was investigated using three different cation-associated extraction methods and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Extraction methods used were the cation exchange resin (CER) method for extracting calcium (Ca2+) and magnesium (Mg2+), sulfide extraction for removing iron, and base treatment (pH 10.5) for dissolving aluminum. Extracellular polymeric substances extracted were then subjected to SDS-PAGE, and the resultant protein profiles were examined before and after sludge digestion. The SDS-PAGE results showed that three methods led to different SDS-PAGE profiles for both undigested and digested sludges. The results further revealed that CER-extracted proteins remained mainly undegraded in anaerobic digestion, but were degraded in aerobic digestion. While the fate of sulfide- and base-extracted proteins was not clear for aerobic digestion, their changes in anaerobic digestion were elucidated. Most sulfide-extracted proteins were removed by anaerobic digestion, while the increase in protein band intensity and diversity was observed for base-extracted proteins. These results suggest that activated sludge flocs contain different fractions of proteins that are distinguishable by their association with certain cations and that each fraction undergoes different fates in anaerobic and aerobic digestion. The proteins that were resistant to degradation and generated during anaerobic digestion were identified by liquid chromatography tandem mass spectrometry. Protein identification results and their putative roles in activated sludge and anaerobic digestion are discussed in this study.
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Affiliation(s)
- Chul Park
- Department of Civil and Environmental Engineering, University of Massachusetts, Amherst, MA 01003, USA.
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Park C, Novak JT, Helm RF, Ahn YO, Esen A. Evaluation of the extracellular proteins in full-scale activated sludges. Water Res 2008; 42:3879-3889. [PMID: 18653206 DOI: 10.1016/j.watres.2008.05.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2008] [Revised: 05/28/2008] [Accepted: 05/30/2008] [Indexed: 05/26/2023]
Abstract
The proteins present in the extracellular polymeric substances (EPS) of activated sludge flocs were investigated using three cation-associated extraction methods. The subproteomes generated from four full-scale activated sludges were subsequently fractionated by ammonium sulfate precipitation and analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). The results showed that each extraction method led to unique SDS-PAGE protein profiles, which provided strong evidence that the extracted proteins are uniquely associated with specific cations in activated sludge flocs. The comparison of protein profiles across sludges from different treatment plants revealed that extracts obtained using a cation-exchange resin exhibited similar protein banding patterns while sulfide- and base-extracted EPS led to more variable protein profiles. Analysis of several SDS-PAGE bands by liquid chromatography-tandem mass spectrometry of tryptic digests led to the identification of several bacterial proteins as well as sewage-derived polypeptides (human elastase IIIA and keratins). Their putative roles in activated sludges and their association with targeted cations are proposed.
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Affiliation(s)
- Chul Park
- Department of Civil and Environmental Engineering, University of Massachusetts, Amherst, MA 01003, USA.
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