1
|
Schuster CD, Salvatore F, Moens L, Martí MA. Globin phylogeny, evolution and function, the newest update. Proteins 2024; 92:720-734. [PMID: 38192262 DOI: 10.1002/prot.26659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/22/2023] [Accepted: 12/15/2023] [Indexed: 01/10/2024]
Abstract
Our globin census update allows us to refine our vision of globin origin, evolution, and structure to function relationship in the context of the currently accepted tree of life. The modern globin domain originates as a single domain, three-over-three α-helical folded structure before the diversification of the kingdoms of life (Bacteria, Archaea, Eukarya). Together with the diversification of prokaryotes, three monophyletic globin families (M, S, and T) emerged, most likely in Proteobacteria and Actinobacteria, displaying specific sequence and structural features, and spread by vertical and horizontal gene transfer, most probably already present in the last universal common ancestor (LUCA). Non-globin domains were added, and eventually lost again, creating multi-domain structures in key branches of M- (FHb and Adgb) and the vast majority of S globins, which with their coevolved multi-domain architectures, have predominantly "sensor" functions. Single domain T-family globins diverged into four major groups and most likely display functions related to reactive nitrogen and oxygen species (RNOS) chemistry, as well as oxygen storage/transport which drives the evolution of its major branches with their characteristic key distal residues (B10, E11, E7, and G8). M-family evolution also lead to distinctive major types (FHb and Fgb, Ngb, Adgb, GbX vertebrate Gbs), and shows the shift from high oxygen affinity controlled by TyrB10-Gln/AsnE11 likely related to RNOS chemistry in microorganisms, to a moderate oxygen affinity storage/transport function controlled by hydrophobic B10/E11-HisE7 in multicellular animals.
Collapse
Affiliation(s)
- Claudio David Schuster
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales (FCEyN), Universidad de Buenos Aires (UBA), Ciudad Autónoma de Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Ciudad Autónoma de Buenos Aires, Argentina
| | - Franco Salvatore
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales (FCEyN), Universidad de Buenos Aires (UBA), Ciudad Autónoma de Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Ciudad Autónoma de Buenos Aires, Argentina
| | - Luc Moens
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Marcelo Adrián Martí
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales (FCEyN), Universidad de Buenos Aires (UBA), Ciudad Autónoma de Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Ciudad Autónoma de Buenos Aires, Argentina
| |
Collapse
|
2
|
Miralles-Robledillo JM, Martínez-Espinosa RM, Pire C. Transcriptomic profiling of haloarchaeal denitrification through RNA-Seq analysis. Appl Environ Microbiol 2024:e0057124. [PMID: 38814058 DOI: 10.1128/aem.00571-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 04/26/2024] [Indexed: 05/31/2024] Open
Abstract
Denitrification, a crucial biochemical pathway prevalent among haloarchaea in hypersaline ecosystems, has garnered considerable attention in recent years due to its ecological implications. Nevertheless, the underlying molecular mechanisms and genetic regulation governing this respiration/detoxification process in haloarchaea remain largely unexplored. In this study, RNA-sequencing was used to compare the transcriptomes of the haloarchaeon Haloferax mediterranei under oxic and denitrifying conditions, shedding light on the intricate metabolic alterations occurring within the cell, such as the accurate control of the metal homeostasis. Furthermore, the investigation identifies several genes encoding transcriptional regulators and potential accessory proteins with putative roles in denitrification. Among these are bacterioopsin-like transcriptional activators, proteins harboring a domain of unknown function (DUF2249), and cyanoglobin. In addition, the study delves into the genetic regulation of denitrification, finding a regulatory motif within promoter regions that activates numerous denitrification-related genes. This research serves as a starting point for future molecular biology studies in haloarchaea, offering a promising avenue to unravel the intricate mechanisms governing haloarchaeal denitrification, a pathway of paramount ecological importance.IMPORTANCEDenitrification, a fundamental process within the nitrogen cycle, has been subject to extensive investigation due to its close association with anthropogenic activities, and its contribution to the global warming issue, mainly through the release of N2O emissions. Although our comprehension of denitrification and its implications is generally well established, most studies have been conducted in non-extreme environments with mesophilic microorganisms. Consequently, there is a significant knowledge gap concerning extremophilic denitrifiers, particularly those inhabiting hypersaline environments. The significance of this research was to delve into the process of haloarchaeal denitrification, utilizing the complete denitrifier haloarchaeon Haloferax mediterranei as a model organism. This research led to the analysis of the metabolic state of this microorganism under denitrifying conditions and the identification of regulatory signals and genes encoding proteins potentially involved in this pathway, serving as a valuable resource for future molecular studies.
Collapse
Affiliation(s)
- Jose María Miralles-Robledillo
- Biochemistry, Molecular Biology, Edaphology and Agricultural Chemistry Department, Faculty of Sciences, Universitat d'Alacant, Alicante, Spain
| | - Rosa María Martínez-Espinosa
- Biochemistry, Molecular Biology, Edaphology and Agricultural Chemistry Department, Faculty of Sciences, Universitat d'Alacant, Alicante, Spain
- Multidisciplinary Institute for Environmental Studies "Ramón Margalef", University of Alicante, Alicante, Spain
| | - Carmen Pire
- Biochemistry, Molecular Biology, Edaphology and Agricultural Chemistry Department, Faculty of Sciences, Universitat d'Alacant, Alicante, Spain
- Multidisciplinary Institute for Environmental Studies "Ramón Margalef", University of Alicante, Alicante, Spain
| |
Collapse
|
3
|
Hoque NJ, Weinert EE. Control of bacterial second messenger signaling and motility by heme-based direct oxygen-sensing proteins. Curr Opin Microbiol 2023; 76:102396. [PMID: 37864983 DOI: 10.1016/j.mib.2023.102396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/15/2023] [Accepted: 09/21/2023] [Indexed: 10/23/2023]
Abstract
Bacteria sense and respond to their environment, allowing them to maximize their survival and growth under changing conditions, such as oxygen levels. Direct oxygen-sensing proteins allow bacteria to rapidly sense concentration changes and adapt by regulating signaling pathways and/or cellular machinery. Recent work has identified roles for direct oxygen-sensing proteins in controlling second messenger levels and motility machinery, as well as effects on biofilm formation, virulence, and motility. In this review, we discuss recent progress in understanding O2-dependent regulation of cyclic di-GMP signaling and motility and highlight the emerging importance in controlling bacterial physiology and behavior.
Collapse
Affiliation(s)
- Nushrat J Hoque
- Department of Chemistry, Penn State University, University Park, PA 16802, USA
| | - Emily E Weinert
- Department of Chemistry, Penn State University, University Park, PA 16802, USA; Department of Biochemistry & Molecular Biology, Penn State University, University Park, PA 16802, USA.
| |
Collapse
|
4
|
Martinez Grundman JE, Johnson EA, Lecomte JTJ. Architectural digest: Thermodynamic stability and domain structure of a consensus monomeric globin. Biophys J 2023; 122:3117-3132. [PMID: 37353934 PMCID: PMC10432219 DOI: 10.1016/j.bpj.2023.06.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 06/13/2023] [Accepted: 06/20/2023] [Indexed: 06/25/2023] Open
Abstract
Artificial proteins representing the consensus of a set of homologous sequences have attracted attention for their increased thermodynamic stability and conserved activity. Here, we applied the consensus approach to a b-type heme-binding protein to inspect the contribution of a dissociable cofactor to enhanced stability and the chemical consequences of creating a generic heme environment. We targeted the group 1 truncated hemoglobin (TrHb1) subfamily of proteins for their small size (∼120 residues) and ease of characterization. The primary structure, derived from a curated set of ∼300 representative sequences, yielded a highly soluble consensus globin (cGlbN) enriched in acidic residues. Optical and NMR spectroscopies revealed high-affinity heme binding in the expected site and in two orientations. At neutral pH, proximal and distal iron coordination was achieved with a pair of histidine residues, as observed in some natural TrHb1s, and with labile ligation on the distal side. As opposed to studied TrHb1s, which undergo additional folding upon heme binding, cGlbN displayed the same extent of secondary structure whether the heme was associated with the protein or not. Denaturation required guanidine hydrochloride and showed that apo- and holoprotein unfolded in two transitions-the first (occurring with a midpoint of ∼2 M) was shifted to higher denaturant concentration in the holoprotein (∼3.7 M) and reflected stabilization due to heme binding, while the second transition (∼6.2 M) was common to both forms. Thus, the consensus sequence stabilized the protein but exposed the existence of two separately cooperative subdomains within the globin architecture, masked as one single domain in TrHb1s with typical stabilities. The results suggested ways in which specific chemical or thermodynamic features may be controlled in artificial heme proteins.
Collapse
Affiliation(s)
| | - Eric A Johnson
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland
| | - Juliette T J Lecomte
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland.
| |
Collapse
|
5
|
Fekete FJ, Marotta NJ, Liu X, Weinert EE. An O 2-sensing diguanylate cyclase broadly affects the aerobic transcriptome in the phytopathogen Pectobacterium carotovorum. Front Microbiol 2023; 14:1134742. [PMID: 37485529 PMCID: PMC10360401 DOI: 10.3389/fmicb.2023.1134742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 06/26/2023] [Indexed: 07/25/2023] Open
Abstract
Pectobacterium carotovorum is an important plant pathogen responsible for the destruction of crops through bacterial soft rot, which is modulated by oxygen (O2) concentration. A soluble globin coupled sensor protein, Pcc DgcO (also referred to as PccGCS) is one way through which P. carotovorum senses oxygen. DgcO contains a diguanylate cyclase output domain producing c-di-GMP. Synthesis of the bacterial second messenger c-di-GMP is increased upon oxygen binding to the sensory globin domain. This work seeks to understand regulation of function by DgcO at the transcript level. RNA sequencing and differential expression analysis revealed that the deletion of DgcO only affects transcript levels in cells grown under aerobic conditions. Differential expression analysis showed that DgcO deletion alters transcript levels for metal transporters. These results, followed by inductively coupled plasma-mass spectrometry showing decreased concentrations of six biologically relevant metals upon DgcO deletion, provide evidence that a globin coupled sensor can affect cellular metal content. These findings improve the understanding of the transcript level control of O2-dependent phenotypes in an important phytopathogen and establish a basis for further studies on c-di-GMP-dependent functions in P. carotovorum.
Collapse
Affiliation(s)
- Florian J. Fekete
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA, United States
| | - Nick J. Marotta
- Graduate Program in Molecular, Cellular, and Integrative Biosciences, Penn State University, University Park, PA, United States
| | - Xuanyu Liu
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA, United States
| | - Emily E. Weinert
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA, United States
- Department of Chemistry, Penn State University, University Park, PA, United States
| |
Collapse
|
6
|
De Simone G, di Masi A, Tundo GR, Coletta M, Ascenzi P. Nitrite Reductase Activity of Ferrous Nitrobindins: A Comparative Study. Int J Mol Sci 2023; 24:ijms24076553. [PMID: 37047528 PMCID: PMC10094804 DOI: 10.3390/ijms24076553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/17/2023] [Accepted: 03/20/2023] [Indexed: 04/03/2023] Open
Abstract
Nitrobindins (Nbs) are all-β-barrel heme proteins spanning from bacteria to Homo sapiens. They inactivate reactive nitrogen species by sequestering NO, converting NO to HNO2, and promoting peroxynitrite isomerization to NO3−. Here, the nitrite reductase activity of Nb(II) from Mycobacterium tuberculosis (Mt-Nb(II)), Arabidopsis thaliana (At-Nb(II)), Danio rerio (Dr-Nb(II)), and Homo sapiens (Hs-Nb(II)) is reported. This activity is crucial for the in vivo production of NO, and thus for the regulation of blood pressure, being of the utmost importance for the blood supply to poorly oxygenated tissues, such as the eye retina. At pH 7.3 and 20.0 °C, the values of the second-order rate constants (i.e., kon) for the reduction of NO2− to NO and the concomitant formation of nitrosylated Mt-Nb(II), At-Nb(II), Dr-Nb(II), and Hs-Nb(II) (Nb(II)-NO) were 7.6 M−1 s−1, 9.3 M−1 s−1, 1.4 × 101 M−1 s−1, and 5.8 M−1 s−1, respectively. The values of kon increased linearly with decreasing pH, thus indicating that the NO2−-based conversion of Nb(II) to Nb(II)-NO requires the involvement of one proton. These results represent the first evidence for the NO2 reductase activity of Nbs(II), strongly supporting the view that Nbs are involved in NO metabolism. Interestingly, the nitrite reductase reactivity of all-β-barrel Nbs and of all-α-helical globins (e.g., myoglobin) was very similar despite the very different three-dimensional fold; however, differences between all-α-helical globins and all-β-barrel Nbs suggest that nitrite reductase activity appears to be controlled by distal steric barriers, even though a more complex regulatory mechanism can be also envisaged.
Collapse
Affiliation(s)
| | | | - Grazia R. Tundo
- Dipartimento di Scienze Cliniche e Medicina Traslazionale, Università di Roma Tor Vergata, 00133 Roma, Italy
| | | | - Paolo Ascenzi
- Laboratorio Interdipartimentale di Microscopia Elettronica, Università Roma Tre, 00146 Roma, Italy
| |
Collapse
|
7
|
Sgammato R, Van Brempt N, Aerts R, Van Doorslaer S, Dewilde S, Herrebout W, Johannessen C. Interaction of nitrite with ferric protoglobin from Methanosarcina acetivorans - an interesting model for spectroscopic studies of the haem-ligand interaction. Dalton Trans 2023; 52:2976-2987. [PMID: 36651272 DOI: 10.1039/d2dt03252j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Protoglobin from Methanosarcina acetivorans (MaPgb) is a dimeric globin belonging to the same lineage of the globin superfamily as globin-coupled sensors. A putative role in the scavenging of reactive nitrogen and oxygen species has been suggested as a possible adaptation mechanism of the host organism to different gaseous environments in the course of evolution. A combination of optical absorption, electronic circular dichroism (ECD), resonance Raman (rRaman), and electron paramagnetic resonance (EPR) reveal the unusual in vitro reaction of ferric MaPgb with nitrite. In contrast to other globins, a large excess of nitrite did not induce the formation of a nitriglobin form in MaPgb. Surprisingly, the addition of nitrite in mildly acidic pH led to the formation of a stable nitric-oxide ligated ferric form of the protein (MaPgb-NO). Furthermore, the 300-700 nm ECD spectrum of ferric MaPgb is for the first time reported and discussed, showing strong differences in the Soret and Q ellipticity compared to ferric myoglobin, in line with the unusually strongly ruffled haem group of MaPgb and the related quantum-mechanical admixture of the S = 5/2 and S = 3/2 state of its ferric form. The Soret and Q ellipticity change strongly upon formation of MaPgb-NO, revealing a significant effect of the nitric-oxide ligation on the haem group and pocket. The related changes in the asymmetric pyrrole half-ring stretching vibration modes observed in the rRaman spectra give experimental support to earlier theoretical models, in which an important role of the in-plane breathing modes of the haem was predicted for the stabilization of the binding of diatomic gases to MaPgb.
Collapse
Affiliation(s)
- Roberta Sgammato
- Laboratory of Molecular Spectroscopy, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium.
| | - Niels Van Brempt
- Laboratory of Biophysics and Biomedical Physics, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium.,Laboratory of Protein Sciences, Proteomics and Epigenetic Signaling, Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Roy Aerts
- Laboratory of Molecular Spectroscopy, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium.
| | - Sabine Van Doorslaer
- Laboratory of Biophysics and Biomedical Physics, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Sylvia Dewilde
- Laboratory of Protein Sciences, Proteomics and Epigenetic Signaling, Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Wouter Herrebout
- Laboratory of Molecular Spectroscopy, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium.
| | - Christian Johannessen
- Laboratory of Molecular Spectroscopy, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium.
| |
Collapse
|
8
|
Queiroz JPF, Lourenzoni MR, Rocha BAM. Structural evolution of an amphibian-specific globin: A computational evolutionary biochemistry approach. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 45:101055. [PMID: 36566682 DOI: 10.1016/j.cbd.2022.101055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
Studies on the globin family are continuously revealing insights into the mechanisms of gene and protein evolution. The rise of a new globin gene type in Pelobatoidea and Neobatrachia (Amphibia:Anura) from an α-globin precursor provides the opportunity to investigate the genetic and physical mechanisms underlying the origin of new protein structural and functional properties. This amphibian-specific globin (globin A/GbA) discovered in the heart of Rana catesbeiana is a monomer. As the ancestral oligomeric state of α-globins is a homodimer, we inferred that the ancestral state was lost somewhere in the GbA lineage. Here, we combined computational molecular evolution with structural bioinformatics to determine the extent to which the loss of the homodimeric state is pervasive in the GbA clade. We also characterized the loci of GbA genes in Bufo bufo. We found two GbA clades in Neobatrachia. One was deleted in Ranidae, but retained and expanded to yield a new globin cluster in Bufonidae species. Loss of the ancestral oligomeric state seems to be pervasive in the GbA clade. However, a taxonomic sampling that includes more Pelobatoidea, as well as early Neobatrachia, lineages would be necessary to determine the oligomeric state of the last common ancestor of all GbA. The evidence presented here points out a possible loss of oligomerization in Pelobatoidea GbA as a result of amino acid substitutions that weaken the homodimeric state. In contrast, the loss of oligomerization in both Neobatrachia GbA clades was linked to independent deletions that disrupted many packing contacts at the homodimer interface.
Collapse
Affiliation(s)
- João Pedro Fernandes Queiroz
- Laboratorio de Biocristalografia - LABIC, Departamento de Bioquimica e Biologia Molecular, Universidade Federal do Ceara, Campus do Pici s.n., bloco 907, Av. Mister Hull, Fortaleza, Ceara, 60440-970, Brazil.
| | - Marcos Roberto Lourenzoni
- Protein Engineering and Health Solutions Group - GEPeSS Fundacao Oswaldo Cruz - Ceara, Eusébio, Ceara, 60175-047, Brazil.
| | - Bruno Anderson Matias Rocha
- Laboratorio de Biocristalografia - LABIC, Departamento de Bioquimica e Biologia Molecular, Universidade Federal do Ceara, Campus do Pici s.n., bloco 907, Av. Mister Hull, Fortaleza, Ceara, 60440-970, Brazil.
| |
Collapse
|
9
|
Defenses of multidrug resistant pathogens against reactive nitrogen species produced in infected hosts. Adv Microb Physiol 2022; 80:85-155. [PMID: 35489794 DOI: 10.1016/bs.ampbs.2022.02.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Bacterial pathogens have sophisticated systems that allow them to survive in hosts in which innate immunity is the frontline of defense. One of the substances produced by infected hosts is nitric oxide (NO) that together with its derived species leads to the so-called nitrosative stress, which has antimicrobial properties. In this review, we summarize the current knowledge on targets and protective systems that bacteria have to survive host-generated nitrosative stress. We focus on bacterial pathogens that pose serious health concerns due to the growing increase in resistance to currently available antimicrobials. We describe the role of nitrosative stress as a weapon for pathogen eradication, the detoxification enzymes, protein/DNA repair systems and metabolic strategies that contribute to limiting NO damage and ultimately allow survival of the pathogen in the host. Additionally, this systematization highlights the lack of available data for some of the most important human pathogens, a gap that urgently needs to be addressed.
Collapse
|
10
|
Schneider T, Tan Y, Li H, Fisher JS, Zhang D. Photoglobin, a distinct family of non-heme binding globins, defines a potential photosensor in prokaryotic signal transduction systems. Comput Struct Biotechnol J 2022; 20:261-273. [PMID: 35024098 PMCID: PMC8717448 DOI: 10.1016/j.csbj.2021.12.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 11/17/2022] Open
Abstract
Globins constitute an ancient superfamily of proteins, exhibiting enormous structural and functional diversity, as demonstrated by many heme-binding families and two non-heme binding families that were discovered in bacterial stressosome component RsbR and in light-harvesting phycobiliproteins (phycocyanin) in cyanobacteria and red algae. By comprehensively exploring the globin repertoire using sensitive computational analyses of sequences, structures, and genomes, we present the identification of the third family of non-heme binding globins—the photoglobin. By conducting profile-based comparisons, clustering analyses, and structural modeling, we demonstrate that photoglobin is related to, but distinct from, the phycocyanin family. Photoglobin preserves a potential ligand-binding pocket, whose residue configuration closely resembles that of phycocyanin, indicating that photoglobin potentially binds to a comparable linear tetrapyrrole. By exploring the contextual information provided by the photoglobin’s domain architectures and gene-neighborhoods, we found that photoglobin is frequently associated with the B12-binding light sensor domain and many domains typical of prokaryotic signal transduction systems. Structural modeling using AlphaFold2 demonstrated that photoglobin and B12-binding domains form a structurally conserved hub among different domain architecture contexts. Based on these strong associations, we predict that the coupled photoglobin and B12-binding domains act as a light-sensing regulatory bundle, with each domain sensing different wavelengths of light resulting in switch-like regulation of downstream signaling effectors. Thus, based on the above lines of evidence, we present a distinct non-heme binding globin family and propose that it may define a new type of light sensor, by means of a linear tetrapyrrole, in complex prokaryotic signal transduction systems.
Collapse
Affiliation(s)
- Theresa Schneider
- Department of Biology, College of Arts & Sciences, Saint Louis University, Saint Louis, MO 63105, United States
| | - Yongjun Tan
- Department of Biology, College of Arts & Sciences, Saint Louis University, Saint Louis, MO 63105, United States
| | - Huan Li
- Department of Biology, College of Arts & Sciences, Saint Louis University, Saint Louis, MO 63105, United States
| | - Jonathan S Fisher
- Department of Biology, College of Arts & Sciences, Saint Louis University, Saint Louis, MO 63105, United States
| | - Dapeng Zhang
- Department of Biology, College of Arts & Sciences, Saint Louis University, Saint Louis, MO 63105, United States.,Program of Bioinformatics and Computational Biology, College of Arts & Sciences, Saint Louis University, MO 63103, United States
| |
Collapse
|
11
|
Kiger L, Keith J, Freiwan A, Fernandez AG, Tillman H, Isakson BE, Weiss MJ, Lechauve C. Redox-Regulation of α-Globin in Vascular Physiology. Antioxidants (Basel) 2022; 11:antiox11010159. [PMID: 35052663 PMCID: PMC8773178 DOI: 10.3390/antiox11010159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 01/07/2022] [Accepted: 01/11/2022] [Indexed: 12/22/2022] Open
Abstract
Interest in the structure, function, and evolutionary relations of circulating and intracellular globins dates back more than 60 years to the first determination of the three-dimensional structure of these proteins. Non-erythrocytic globins have been implicated in circulatory control through reactions that couple nitric oxide (NO) signaling with cellular oxygen availability and redox status. Small artery endothelial cells (ECs) express free α-globin, which causes vasoconstriction by degrading NO. This reaction converts reduced (Fe2+) α-globin to the oxidized (Fe3+) form, which is unstable, cytotoxic, and unable to degrade NO. Therefore, (Fe3+) α-globin must be stabilized and recycled to (Fe2+) α-globin to reinitiate the catalytic cycle. The molecular chaperone α-hemoglobin-stabilizing protein (AHSP) binds (Fe3+) α-globin to inhibit its degradation and facilitate its reduction. The mechanisms that reduce (Fe3+) α-globin in ECs are unknown, although endothelial nitric oxide synthase (eNOS) and cytochrome b5 reductase (CyB5R3) with cytochrome b5 type A (CyB5a) can reduce (Fe3+) α-globin in solution. Here, we examine the expression and cellular localization of eNOS, CyB5a, and CyB5R3 in mouse arterial ECs and show that α-globin can be reduced by either of two independent redox systems, CyB5R3/CyB5a and eNOS. Together, our findings provide new insights into the regulation of blood vessel contractility.
Collapse
Affiliation(s)
- Laurent Kiger
- Inserm U955, Institut Mondor de Recherche Biomédicale, University Paris Est Creteil, 94017 Créteil, France;
| | - Julia Keith
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (J.K.); (A.G.F.); (M.J.W.)
| | - Abdullah Freiwan
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA;
| | - Alfonso G. Fernandez
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (J.K.); (A.G.F.); (M.J.W.)
| | - Heather Tillman
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA;
| | - Brant E. Isakson
- Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA 22908, USA;
| | - Mitchell J. Weiss
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (J.K.); (A.G.F.); (M.J.W.)
| | - Christophe Lechauve
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (J.K.); (A.G.F.); (M.J.W.)
- Correspondence: ; Tel.: +1-(901)-595-8344; Fax: +1-(901)-595-4723
| |
Collapse
|
12
|
Nardini M, Pesce A, Bolognesi M. Truncated (2/2) hemoglobin: Unconventional structures and functional roles in vivo and in human pathogenesis. Mol Aspects Med 2021; 84:101049. [PMID: 34776271 DOI: 10.1016/j.mam.2021.101049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/02/2021] [Accepted: 11/03/2021] [Indexed: 12/12/2022]
Abstract
Truncated hemoglobins (trHbs) build a sub-class of the globin family, found in eubacteria, cyanobacteria, unicellular eukaryotes, and in higher plants; among these, selected human pathogens are found. The trHb fold is based on a 2/2 α-helical sandwich, consisting of a simplified and reduced-size version of the classical 3/3 α-helical sandwich of vertebrate and invertebrate globins. Phylogenetic analysis indicates that trHbs further branch into three groups: group I (or trHbN), group II (or trHbO), and group III (or trHbP), each group being characterized by specific structural features. Among these, a protein matrix tunnel, or a cavity system implicated in diatomic ligand diffusion through the protein matrix, is typical of group I and group II, respectively. In general, a highly intertwined network of hydrogen bonds stabilizes the heme bound ligand, despite variability of the heme distal residues in the different trHb groups. Notably, some organisms display genes from more than one trHb group, suggesting that trHbN, trHbO, and trHbP may support different functions in vivo, such as detoxification of reactive nitrogen and oxygen species, respiration, oxygen storage/sensoring, thus aiding survival of an invading microorganism. Here, structural features and proposed functions of trHbs from human pathogens are reviewed.
Collapse
Affiliation(s)
- Marco Nardini
- Department of Biosciences, University of Milano, Milano, Italy
| | | | | |
Collapse
|
13
|
Patterson DC, Ruiz MP, Yoon H, Walker JA, Armache JP, Yennawar NH, Weinert EE. Differential ligand-selective control of opposing enzymatic activities within a bifunctional c-di-GMP enzyme. Proc Natl Acad Sci U S A 2021; 118:e2100657118. [PMID: 34475207 PMCID: PMC8433548 DOI: 10.1073/pnas.2100657118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 08/02/2021] [Indexed: 01/23/2023] Open
Abstract
Cyclic dimeric guanosine monophosphate (c-di-GMP) serves as a second messenger that modulates bacterial cellular processes, including biofilm formation. While proteins containing both c-di-GMP synthesizing (GGDEF) and c-di-GMP hydrolyzing (EAL) domains are widely predicted in bacterial genomes, it is poorly understood how domains with opposing enzymatic activity are regulated within a single polypeptide. Herein, we report the characterization of a globin-coupled sensor protein (GCS) from Paenibacillus dendritiformis (DcpG) with bifunctional c-di-GMP enzymatic activity. DcpG contains a regulatory sensor globin domain linked to diguanylate cyclase (GGDEF) and phosphodiesterase (EAL) domains that are differentially regulated by gas binding to the heme; GGDEF domain activity is activated by the Fe(II)-NO state of the globin domain, while EAL domain activity is activated by the Fe(II)-O2 state. The in vitro activity of DcpG is mimicked in vivo by the biofilm formation of P. dendritiformis in response to gaseous environment, with nitric oxide conditions leading to the greatest amount of biofilm formation. The ability of DcpG to differentially control GGDEF and EAL domain activity in response to ligand binding is likely due to the unusual properties of the globin domain, including rapid ligand dissociation rates and high midpoint potentials. Using structural information from small-angle X-ray scattering and negative stain electron microscopy studies, we developed a structural model of DcpG, providing information about the regulatory mechanism. These studies provide information about full-length GCS protein architecture and insight into the mechanism by which a single regulatory domain can selectively control output domains with opposing enzymatic activities.
Collapse
Affiliation(s)
- Dayna C Patterson
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
| | - Myrrh Perez Ruiz
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
| | - Hyerin Yoon
- Department of Chemistry, Emory University, Atlanta, GA 30322
| | | | - Jean-Paul Armache
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Neela H Yennawar
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Emily E Weinert
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802;
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
| |
Collapse
|
14
|
Keller TCS, Lechauve C, Keller AS, Brooks S, Weiss MJ, Columbus L, Ackerman HC, Cortese-Krott MM, Isakson BE. The role of globins in cardiovascular physiology. Physiol Rev 2021; 102:859-892. [PMID: 34486392 DOI: 10.1152/physrev.00037.2020] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Globin proteins exist in every cell type of the vasculature, from erythrocytes to endothelial cells, vascular smooth muscle cells, and peripheral nerve cells. Many globin subtypes are also expressed in muscle tissues (including cardiac and skeletal muscle), in other organ-specific cell types, and in cells of the central nervous system. The ability of each of these globins to interact with molecular oxygen (O2) and nitric oxide (NO) is preserved across these contexts. Endothelial α-globin is an example of extra-erythrocytic globin expression. Other globins, including myoglobin, cytoglobin, and neuroglobin are observed in other vascular tissues. Myoglobin is observed primarily in skeletal muscle and smooth muscle cells surrounding the aorta or other large arteries. Cytoglobin is found in vascular smooth muscle but can also be expressed in non-vascular cell types, especially in oxidative stress conditions after ischemic insult. Neuroglobin was first observed in neuronal cells, and its expression appears to be restricted mainly to the central and peripheral nervous systems. Brain and central nervous system neurons expressing neuroglobin are positioned close to many arteries within the brain parenchyma and can control smooth muscle contraction and, thus, tissue perfusion and vascular reactivity. Overall, reactions between NO and globin heme-iron contribute to vascular homeostasis by regulating vasodilatory NO signals and scaveging reactive species in cells of the mammalian vascular system. Here, we discuss how globin proteins affect vascular physiology with a focus on NO biology, and offer perspectives for future study of these functions.
Collapse
Affiliation(s)
- T C Steven Keller
- Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, United States.,Department of Molecular Physiology and Biophysics, University of Virginia School of Medicine, Charlottesville, VA, United States
| | - Christophe Lechauve
- Department of Hematology, St. Jude's Children's Research Hospital, Memphis, TN, United States
| | - Alexander S Keller
- Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, United States.,Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA, United States
| | - Steven Brooks
- Physiology Unit, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Rockville, MD, United States
| | - Mitchell J Weiss
- Department of Hematology, St. Jude's Children's Research Hospital, Memphis, TN, United States
| | - Linda Columbus
- Department of Chemistry, University of Virginia, Charlottesville, VA, United States
| | - Hans C Ackerman
- Physiology Unit, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Rockville, MD, United States
| | - Miriam M Cortese-Krott
- Myocardial Infarction Research Laboratory, Department of Cardiology, Pulmunology, and Angiology, Medical Faculty, Heinrich-Heine-University of Düsseldorf, Düsseldorf, Germany.,Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Brant E Isakson
- Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, United States.,Department of Molecular Physiology and Biophysics, University of Virginia School of Medicine, Charlottesville, VA, United States
| |
Collapse
|
15
|
Borisov VB, Siletsky SA, Paiardini A, Hoogewijs D, Forte E, Giuffrè A, Poole RK. Bacterial Oxidases of the Cytochrome bd Family: Redox Enzymes of Unique Structure, Function, and Utility As Drug Targets. Antioxid Redox Signal 2021; 34:1280-1318. [PMID: 32924537 PMCID: PMC8112716 DOI: 10.1089/ars.2020.8039] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 09/01/2020] [Accepted: 09/02/2020] [Indexed: 12/23/2022]
Abstract
Significance: Cytochrome bd is a ubiquinol:oxygen oxidoreductase of many prokaryotic respiratory chains with a unique structure and functional characteristics. Its primary role is to couple the reduction of molecular oxygen, even at submicromolar concentrations, to water with the generation of a proton motive force used for adenosine triphosphate production. Cytochrome bd is found in many bacterial pathogens and, surprisingly, in bacteria formally denoted as anaerobes. It endows bacteria with resistance to various stressors and is a potential drug target. Recent Advances: We summarize recent advances in the biochemistry, structure, and physiological functions of cytochrome bd in the light of exciting new three-dimensional structures of the oxidase. The newly discovered roles of cytochrome bd in contributing to bacterial protection against hydrogen peroxide, nitric oxide, peroxynitrite, and hydrogen sulfide are assessed. Critical Issues: Fundamental questions remain regarding the precise delineation of electron flow within this multihaem oxidase and how the extraordinarily high affinity for oxygen is accomplished, while endowing bacteria with resistance to other small ligands. Future Directions: It is clear that cytochrome bd is unique in its ability to confer resistance to toxic small molecules, a property that is significant for understanding the propensity of pathogens to possess this oxidase. Since cytochrome bd is a uniquely bacterial enzyme, future research should focus on harnessing fundamental knowledge of its structure and function to the development of novel and effective antibacterial agents.
Collapse
Affiliation(s)
- Vitaliy B. Borisov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Sergey A. Siletsky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
| | | | - David Hoogewijs
- Department of Medicine/Physiology, University of Fribourg, Fribourg, Switzerland
| | - Elena Forte
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | | | - Robert K. Poole
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, United Kingdom
| |
Collapse
|
16
|
Durand S, Guillier M. Transcriptional and Post-transcriptional Control of the Nitrate Respiration in Bacteria. Front Mol Biosci 2021; 8:667758. [PMID: 34026838 PMCID: PMC8139620 DOI: 10.3389/fmolb.2021.667758] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 03/29/2021] [Indexed: 12/02/2022] Open
Abstract
In oxygen (O2) limiting environments, numerous aerobic bacteria have the ability to shift from aerobic to anaerobic respiration to release energy. This process requires alternative electron acceptor to replace O2 such as nitrate (NO3 -), which has the next best reduction potential after O2. Depending on the organism, nitrate respiration involves different enzymes to convert NO3 - to ammonium (NH4 +) or dinitrogen (N2). The expression of these enzymes is tightly controlled by transcription factors (TFs). More recently, bacterial small regulatory RNAs (sRNAs), which are important regulators of the rapid adaptation of microorganisms to extremely diverse environments, have also been shown to control the expression of genes encoding enzymes or TFs related to nitrate respiration. In turn, these TFs control the synthesis of multiple sRNAs. These results suggest that sRNAs play a central role in the control of these metabolic pathways. Here we review the complex interplay between the transcriptional and the post-transcriptional regulators to efficiently control the respiration on nitrate.
Collapse
Affiliation(s)
- Sylvain Durand
- CNRS, UMR 8261, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
| | - Maude Guillier
- CNRS, UMR 8261, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
| |
Collapse
|
17
|
Uppal S, Khan MA, Kundu S. Stability and Folding of the Unusually Stable Hemoglobin from Synechocystis is Subtly Optimized and Dependent on the Key Heme Pocket Residues. Protein Pept Lett 2021; 28:164-182. [PMID: 32533815 DOI: 10.2174/0929866527666200613220245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/20/2020] [Accepted: 04/24/2020] [Indexed: 11/22/2022]
Abstract
AIMS The aim of our study is to understand the biophysical traits that govern the stability and folding of Synechocystis hemoglobin, a unique cyanobacterial globin that displays unusual traits not observed in any of the other globins discovered so far. BACKGROUND For the past few decades, classical hemoglobins such as vertebrate hemoglobin and myoglobin have been extensively studied to unravel the stability and folding mechanisms of hemoglobins. However, the expanding wealth of hemoglobins identified in all life forms with novel properties, like heme coordination chemistry and globin fold, have added complexity and challenges to the understanding of hemoglobin stability, which has not been adequately addressed. Here, we explored the unique truncated and hexacoordinate hemoglobin from the freshwater cyanobacterium Synechocystis sp. PCC 6803 known as "Synechocystis hemoglobin (SynHb)". The "three histidines" linkages to heme are novel to this cyanobacterial hemoglobin. OBJECTIVE Mutational studies were employed to decipher the residues within the heme pocket that dictate the stability and folding of SynHb. METHODS Site-directed mutants of SynHb were generated and analyzed using a repertoire of spectroscopic and calorimetric tools. RESULTS The results revealed that the heme was stably associated to the protein under all denaturing conditions with His117 playing the anchoring role. The studies also highlighted the possibility of existence of a "molten globule" like intermediate at acidic pH in this exceptionally thermostable globin. His117 and other key residues in the heme pocket play an indispensable role in imparting significant polypeptide stability. CONCLUSION Synechocystis hemoglobin presents an important model system for investigations of protein folding and stability in general. The heme pocket residues influenced the folding and stability of SynHb in a very subtle and specific manner and may have been optimized to make this Hb the most stable known as of date. Other: The knowledge gained hereby about the influence of heme pocket amino acid side chains on stability and expression is currently being utilized to improve the stability of recombinant human Hbs for efficient use as oxygen delivery vehicles.
Collapse
Affiliation(s)
- Sheetal Uppal
- Department of Biochemistry, University of Delhi South Campus, New Delhi, 110021, India
| | - Mohd Asim Khan
- Department of Biochemistry, University of Delhi South Campus, New Delhi, 110021, India
| | - Suman Kundu
- Department of Biochemistry, University of Delhi South Campus, New Delhi, 110021, India
| |
Collapse
|
18
|
Julió Plana L, Martinez Grundman JE, Estrin DA, Lecomte JTJ, Capece L. Distal lysine (de)coordination in the algal hemoglobin THB1: A combined computer simulation and experimental study. J Inorg Biochem 2021; 220:111455. [PMID: 33882423 DOI: 10.1016/j.jinorgbio.2021.111455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 03/26/2021] [Accepted: 03/27/2021] [Indexed: 11/26/2022]
Abstract
THB1 is a monomeric truncated hemoglobin from the green alga Chlamydomonas reinhardtii. In the absence of exogenous ligands and at neutral pH, the heme group of THB1 is coordinated by two protein residues, Lys53 and His77. THB1 is thought to function as a nitric oxide dioxygenase, and the distal binding of O2 requires the cleavage of the Fe-Lys53 bond accompanied by protonation and expulsion of the lysine from the heme cavity into the solvent. Nuclear magnetic resonance spectroscopy and crystallographic data have provided dynamic and structural insights of the process, but the details of the mechanism have not been fully elucidated. We applied a combination of computer simulations and site-directed mutagenesis experiments to shed light on this issue. Molecular dynamics simulations and hybrid quantum mechanics/molecular mechanics restrained optimizations were performed to explore the nature of the transition between the decoordinated and lysine-bound states of the ferrous heme in THB1. Lys49 and Arg52, which form ionic interactions with the heme propionates in the X-ray structure of lysine-bound THB1, were observed to assist in maintaining Lys53 inside the protein cavity and play a key role in the transition. Lys49Ala, Arg52Ala and Lys49Ala/Arg52Ala THB1 variants were prepared, and the consequences of the replacements on the Lys (de)coordination equilibrium were characterized experimentally for comparison with computational prediction. The results reinforced the dynamic role of protein-propionate interactions and strongly suggested that cleavage of the Fe-Lys53 bond and ensuing conformational rearrangement is facilitated by protonation of the amino group inside the distal cavity.
Collapse
Affiliation(s)
- Laia Julió Plana
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Jaime E Martinez Grundman
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, United States
| | - Darío A Estrin
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Juliette T J Lecomte
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, United States.
| | - Luciana Capece
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.
| |
Collapse
|
19
|
Hammerschmid D, Germani F, Drusin SI, Fagnen C, Schuster CD, Hoogewijs D, Marti MA, Venien-Bryan C, Moens L, Van Doorslaer S, Sobott F, Dewilde S. Structural modeling of a novel membrane-bound globin-coupled sensor in Geobacter sulfurreducens. Comput Struct Biotechnol J 2021; 19:1874-1888. [PMID: 33995893 PMCID: PMC8076648 DOI: 10.1016/j.csbj.2021.03.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 03/24/2021] [Accepted: 03/24/2021] [Indexed: 12/12/2022] Open
Abstract
Globin-coupled sensors (GCS) usually consist of three domains: a sensor/globin, a linker, and a transmitter domain. The globin domain (GD), activated by ligand binding and/or redox change, induces an intramolecular signal transduction resulting in a response of the transmitter domain. Depending on the nature of the transmitter domain, GCSs can have different activities and functions, including adenylate and di-guanylate cyclase, histidine kinase activity, aerotaxis and/or oxygen sensing function. The gram-negative delta-proteobacterium Geobacter sulfurreducens expresses a protein with a GD covalently linked to a four transmembrane domain, classified, by sequence similarity, as GCS (GsGCS). While its GD is fully characterized, not so its transmembrane domain, which is rarely found in the globin superfamily. In the present work, GsGCS was characterized spectroscopically and by native ion mobility-mass spectrometry in combination with cryo-electron microscopy. Although lacking high resolution, the oligomeric state and the electron density map were valuable for further rational modeling of the full-length GsGCS structure. This model demonstrates that GsGCS forms a transmembrane domain-driven tetramer with minimal contact between the GDs and with the heme groups oriented outward. This organization makes an intramolecular signal transduction less likely. Our results, including the auto-oxidation rate and redox potential, suggest a potential role for GsGCS as redox sensor or in a membrane-bound e-/H+ transfer. As such, GsGCS might act as a player in connecting energy production to the oxidation of organic compounds and metal reduction. Database searches indicate that GDs linked to a four or seven helices transmembrane domain occur more frequently than expected.
Collapse
Key Words
- AfGcHK, Anaeromyxobacter sp. Fw109-5 GcHK
- AsFRMF, Ascaris suum FRMF-amide receptor
- AvGReg, Azotobacter vinilandii Greg
- BpGReg, Bordetella pertussis Greg
- BsHemAT, Bacillus subtilis HemAT
- CCS, collision cross section
- CIU, collision-induced unfolding
- CMC, critical micelle concentration
- CV, cyclic voltammetry
- CeGLB26, Caenorhabditis elegans globin 26
- CeGLB33, Caenorhabditis elegans globin 33
- CeGLB6, Caenorhabditis elegans globin 6
- DDM, n-dodecyl-β-d-maltoside
- DPV, differential pulse voltammetry
- EcDosC, Escherichia coli Dos with DGC activity
- FMRF, H-Phe-Met-Arg-Phe-NH2 neuropeptide
- GCS, globin-coupled sensor
- GD, globin domain
- GGDEF, Gly-Gly-Asp-Glu-Phe motive
- Gb, globin
- Geobacter sulfurreducens
- GintHb, hemoglobin from Gasterophilus intestinalis
- Globin-coupled sensor
- GsGCS, Geobacter sulfurreducens GCS
- GsGCS162, GD of GsGCS
- IM-MS, ion mobility-mass spectrometry
- LmHemAC, Leishmania major HemAC
- MaPgb, Methanosarcina acetivorans protoglobin
- MtTrHbO, Mycobacterium tuberculosis truncated hemoglobin O
- NH4OAc, ammonium acetate
- OG, n-octyl-β-d-glucopyranoside
- PDE, phosphodiesterase
- PcMb, Physether catodon myoglobin
- PccGCS, Pectobacterium carotivorum GCS
- PsiE, phosphate-starvation-inducible E
- RR, resonance Raman
- SCE, saturated calomel electrode
- SHE, standard hydrogen electrode
- SaktrHb, Streptomyces avermitilis truncated hemoglobin-antibiotic monooxygenase
- SwMb, myoglobin from sperm whale
- TD, Transmitter domain
- TmD, Transmembrane domain
- Transmembrane domain
- Transmembrane-coupled globins
- mNgb, mouse neuroglobin
Collapse
Affiliation(s)
- Dietmar Hammerschmid
- Proteinchemistry, Proteomics and Epigenetic Signalling, Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
- Biomolecular & Analytical Mass Spectrometry, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Francesca Germani
- Proteinchemistry, Proteomics and Epigenetic Signalling, Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Salvador I. Drusin
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellòn 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
| | - Charline Fagnen
- Sorbonne Université, UMR 7590, CNRS, Muséum National d’Histoire Naturelle, Institut de Minéralogie, Physique des Matériaux et Cosmochimie, IMPMC, 75005 Paris, France
| | - Claudio D. Schuster
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellòn 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
| | - David Hoogewijs
- Section of Medicine, Department of Endocrinology, Metabolism and Cardiovascular System, University of Fribourg, Switzerland
| | - Marcelo A. Marti
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellòn 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
| | - Catherine Venien-Bryan
- Sorbonne Université, UMR 7590, CNRS, Muséum National d’Histoire Naturelle, Institut de Minéralogie, Physique des Matériaux et Cosmochimie, IMPMC, 75005 Paris, France
| | - Luc Moens
- Proteinchemistry, Proteomics and Epigenetic Signalling, Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Sabine Van Doorslaer
- Biophysics and Biomedical Physics, Department of Chemistry, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Frank Sobott
- Biomolecular & Analytical Mass Spectrometry, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
- School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, United Kingdom
| | - Sylvia Dewilde
- Proteinchemistry, Proteomics and Epigenetic Signalling, Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| |
Collapse
|
20
|
Belato FA, Coates CJ, Halanych KM, Weber RE, Costa-Paiva EM. Evolutionary History of the Globin Gene Family in Annelids. Genome Biol Evol 2020; 12:1719-1733. [PMID: 32597988 PMCID: PMC7549130 DOI: 10.1093/gbe/evaa134] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/22/2020] [Indexed: 12/20/2022] Open
Abstract
Animals depend on the sequential oxidation of organic molecules to survive; thus, oxygen-carrying/transporting proteins play a fundamental role in aerobic metabolism. Globins are the most common and widespread group of respiratory proteins. They can be divided into three types: circulating intracellular, noncirculating intracellular, and extracellular, all of which have been reported in annelids. The diversity of oxygen transport proteins has been underestimated across metazoans. We probed 250 annelid transcriptomes in search of globin diversity in order to elucidate the evolutionary history of this gene family within this phylum. We report two new globin types in annelids, namely androglobins and cytoglobins. Although cytoglobins and myoglobins from vertebrates and from invertebrates are referred to by the same name, our data show they are not genuine orthologs. Our phylogenetic analyses show that extracellular globins from annelids are more closely related to extracellular globins from other metazoans than to the intracellular globins of annelids. Broadly, our findings indicate that multiple gene duplication and neo-functionalization events shaped the evolutionary history of the globin family.
Collapse
Affiliation(s)
- Flávia A Belato
- Department of Zoology, Institute of Biosciences, University of Sao Paulo, Brazil
| | - Christopher J Coates
- Department of Biosciences, College of Science, Swansea University, United Kingdom
| | - Kenneth M Halanych
- Department of Biological Sciences, Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University
| | - Roy E Weber
- Zoophysiology, Department of Biology, Aarhus University, Denmark
| | - Elisa M Costa-Paiva
- Department of Zoology, Institute of Biosciences, University of Sao Paulo, Brazil
| |
Collapse
|
21
|
Becana M, Yruela I, Sarath G, Catalán P, Hargrove MS. Plant hemoglobins: a journey from unicellular green algae to vascular plants. THE NEW PHYTOLOGIST 2020; 227:1618-1635. [PMID: 31960995 DOI: 10.1111/nph.16444] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 12/24/2019] [Indexed: 05/17/2023]
Abstract
Globins (Glbs) are widely distributed in archaea, bacteria and eukaryotes. They can be classified into proteins with 2/2 or 3/3 α-helical folding around the heme cavity. Both types of Glbs occur in green algae, bryophytes and vascular plants. The Glbs of angiosperms have been more intensively studied, and several protein structures have been solved. They can be hexacoordinate or pentacoordinate, depending on whether a histidine is coordinating or not at the sixth position of the iron atom. The 3/3 Glbs of class 1 and the 2/2 Glbs (also called class 3 in plants) are present in all angiosperms, whereas the 3/3 Glbs of class 2 have been only found in early angiosperms and eudicots. The three Glb classes are expected to play different roles. Class 1 Glbs are involved in hypoxia responses and modulate NO concentration, which may explain their roles in plant morphogenesis, hormone signaling, cell fate determination, nutrient deficiency, nitrogen metabolism and plant-microorganism symbioses. Symbiotic Glbs derive from class 1 or class 2 Glbs and transport O2 in nodules. The physiological roles of class 2 and class 3 Glbs are poorly defined but could involve O2 and NO transport and/or metabolism, respectively. More research is warranted on these intriguing proteins to determine their non-redundant functions.
Collapse
Affiliation(s)
- Manuel Becana
- Departamento de Nutrición Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas (CSIC), Apartado 13034, 50080, Zaragoza, Spain
| | - Inmaculada Yruela
- Departamento de Nutrición Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas (CSIC), Apartado 13034, 50080, Zaragoza, Spain
- Group of Biochemistry, Biophysics and Computational Biology (BIFI-Unizar) Joint Unit to CSIC, Edificio I+D Campus Río Ebro, 50018, Zaragoza, Spain
| | - Gautam Sarath
- Wheat, Sorghum, and Forage Research Unit, USDA-ARS, East Campus, University of Nebraska-Lincoln, Lincoln, NE, 86583, USA
| | - Pilar Catalán
- Group of Biochemistry, Biophysics and Computational Biology (BIFI-Unizar) Joint Unit to CSIC, Edificio I+D Campus Río Ebro, 50018, Zaragoza, Spain
- Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, 22071, Huesca, Spain
| | - Mark S Hargrove
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| |
Collapse
|
22
|
Lessons from the post-genomic era: Globin diversity beyond oxygen binding and transport. Redox Biol 2020; 37:101687. [PMID: 32863222 PMCID: PMC7475203 DOI: 10.1016/j.redox.2020.101687] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/11/2020] [Accepted: 08/11/2020] [Indexed: 12/16/2022] Open
Abstract
Vertebrate hemoglobin (Hb) and myoglobin (Mb) were among the first proteins whose structures and sequences were determined over 50 years ago. In the subsequent pregenomic period, numerous related proteins came to light in plants, invertebrates and bacteria, that shared the myoglobin fold, a signature sequence motif characteristic of a 3-on-3 α-helical sandwich. Concomitantly, eukaryote and bacterial globins with a truncated 2-on-2 α-helical fold were discovered. Genomic information over the last 20 years has dramatically expanded the list of known globins, demonstrating their existence in a limited number of archaeal genomes, a majority of bacterial genomes and an overwhelming majority of eukaryote genomes. In vertebrates, 6 additional globin types were identified, namely neuroglobin (Ngb), cytoglobin (Cygb), globin E (GbE), globin X (GbX), globin Y (GbY) and androglobin (Adgb). Furthermore, functions beyond the familiar oxygen transport and storage have been discovered within the vertebrate globin family, including NO metabolism, peroxidase activity, scavenging of free radicals, and signaling functions. The extension of the knowledge on globin functions suggests that the original roles of bacterial globins must have been enzymatic, involved in defense against NO toxicity, and perhaps also as sensors of O2, regulating taxis away or towards high O2 concentrations. In this review, we aimed to discuss the evolution and remarkable functional diversity of vertebrate globins with particular focus on the variety of non-canonical expression sites of mammalian globins and their according impressive variability of atypical functions.
Collapse
|
23
|
Finoshin AD, Adameyko KI, Mikhailov KV, Kravchuk OI, Georgiev AA, Gornostaev NG, Kosevich IA, Mikhailov VS, Gazizova GR, Shagimardanova EI, Gusev OA, Lyupina YV. Iron metabolic pathways in the processes of sponge plasticity. PLoS One 2020; 15:e0228722. [PMID: 32084159 PMCID: PMC7034838 DOI: 10.1371/journal.pone.0228722] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 01/21/2020] [Indexed: 12/11/2022] Open
Abstract
The ability to regulate oxygen consumption evolved in ancestral animals and is intrinsically linked to iron metabolism. The iron pathways have been intensively studied in mammals, whereas data on distant invertebrates are limited. Sea sponges represent the oldest animal phylum and have unique structural plasticity and capacity to reaggregate after complete dissociation. We studied iron metabolic factors and their expression during reaggregation in the White Sea cold-water sponges Halichondria panicea and Halisarca dujardini. De novo transcriptomes were assembled using RNA-Seq data, and evolutionary trends were analyzed with bioinformatic tools. Differential expression during reaggregation was studied for H. dujardini. Enzymes of the heme biosynthesis pathway and transport globins, neuroglobin (NGB) and androglobin (ADGB), were identified in sponges. The globins mutate at higher evolutionary rates than the heme synthesis enzymes. Highly conserved iron-regulatory protein 1 (IRP1) presumably interacts with the iron-responsive elements (IREs) found in mRNAs of ferritin (FTH1) and a putative transferrin receptor NAALAD2. The reaggregation process is accompanied by increased expression of IRP1, the antiapoptotic factor BCL2, the inflammation factor NFκB (p65), FTH1 and NGB, as well as by an increase in mitochondrial density. Our data indicate a complex mechanism of iron regulation in sponge structural plasticity and help to better understand general mechanisms of morphogenetic processes in multicellular species.
Collapse
Affiliation(s)
- Alexander D. Finoshin
- N.K. Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia
| | - Kim I. Adameyko
- N.K. Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia
| | - Kirill V. Mikhailov
- A.N. Belozersky Institute of Physical and Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Oksana I. Kravchuk
- N.K. Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - Nicolay G. Gornostaev
- N.K. Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - Victor S. Mikhailov
- N.K. Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia
| | | | | | - Oleg A. Gusev
- Kazan Federal University, Kazan, Russia
- KFU-RIKEN Translational Genomics Unit, RIKEN National Science Institute, Yokohama, Japan
| | - Yulia V. Lyupina
- N.K. Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia
| |
Collapse
|
24
|
Giordano D, Boubeta FM, di Prisco G, Estrin DA, Smulevich G, Viappiani C, Verde C. Conformational Flexibility Drives Cold Adaptation in Pseudoalteromonas haloplanktis TAC125 Globins. Antioxid Redox Signal 2020; 32:396-411. [PMID: 31578873 DOI: 10.1089/ars.2019.7887] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Significance: Temperature is one of the most important drivers in shaping protein adaptations. Many biochemical and physiological processes are influenced by temperature. Proteins and enzymes from organisms living at low temperature are less stable in comparison to high-temperature adapted proteins. The lower stability is generally due to greater conformational flexibility. Recent Advances: Adaptive changes in the structure of cold-adapted proteins may occur at subunit interfaces, distant from the active site, thus producing energy changes associated with conformational transitions transmitted to the active site by allosteric modulation, valid also for monomeric proteins in which tertiary structural changes may play an essential role. Critical Issues: Despite efforts, the current experimental and computational methods still fail to produce general principles on protein evolution, since many changes are protein and species dependent. Environmental constraints or other biological cellular signals may override the ancestral information included in the structure of the protein, thus introducing inaccuracy in estimates and predictions on the evolutionary adaptations of proteins in response to cold adaptation. Future Directions: In this review, we describe the studies and approaches used to investigate stability and flexibility in the cold-adapted globins of the Antarctic marine bacterium Pseudoalteromonas haloplanktis TAC125. In fact, future research directions will be prescient on more detailed investigation of cold-adapted proteins and the role of fluctuations between different conformational states.
Collapse
Affiliation(s)
- Daniela Giordano
- Institute of Biosciences and BioResources (IBBR), CNR, Napoli, Italy.,Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Fernando Martín Boubeta
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Guido di Prisco
- Institute of Biosciences and BioResources (IBBR), CNR, Napoli, Italy
| | - Dario A Estrin
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | | | - Cristiano Viappiani
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parma, Italy
| | - Cinzia Verde
- Institute of Biosciences and BioResources (IBBR), CNR, Napoli, Italy.,Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
| |
Collapse
|
25
|
Distinctive structural properties of THB11, a pentacoordinate Chlamydomonas reinhardtii truncated hemoglobin with N- and C-terminal extensions. J Biol Inorg Chem 2020; 25:267-283. [PMID: 32048044 PMCID: PMC7082302 DOI: 10.1007/s00775-020-01759-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 01/14/2020] [Indexed: 12/20/2022]
Abstract
Hemoglobins (Hbs) utilize heme b as a cofactor and are found in all kingdoms of life. The current knowledge reveals an enormous variability of Hb primary sequences, resulting in topological, biochemical and physiological individuality. As Hbs appear to modulate their reactivities through specific combinations of structural features, predicting the characteristics of a given Hb is still hardly possible. The unicellular green alga Chlamydomonas reinhardtii contains 12 genes encoding diverse Hbs of the truncated lineage, several of which possess extended N- or C-termini of unknown function. Studies on some of the Chlamydomonas Hbs revealed yet unpredictable structural and biochemical variations, which, along with a different expression of their genes, suggest diverse physiological roles. Chlamydomonas thus represents a promising system to analyze the diversification of Hb structure, biochemistry and physiology. Here, we report the crystal structure, resolved to 1.75 Å, of the heme-binding domain of cyanomet THB11 (Cre16.g662750), one of the pentacoordinate algal Hbs, which offer a free Fe-coordination site in the reduced state. The overall fold of THB11 is conserved, but individual features such as a kink in helix E, a tilted heme plane and a clustering of methionine residues at a putative tunnel exit appear to be unique. Both N- and C-termini promote the formation of oligomer mixtures, and the absence of the C terminus results in reduced nitrite reduction rates. This work widens the structural and biochemical knowledge on the 2/2Hb family and suggests that the N- and C-terminal extensions of the Chlamydomonas 2/2Hbs modulate their reactivity by intermolecular interactions.
Collapse
|
26
|
Abstract
Flavohaemoglobins were first described in yeast as early as the 1970s but their functions were unclear. The surge in interest in nitric oxide biology and both serendipitous and hypothesis-driven discoveries in bacterial systems have transformed our understanding of this unusual two-domain globin into a comprehensive, yet undoubtedly incomplete, appreciation of its pre-eminent role in nitric oxide detoxification. Here, I focus on research on the flavohaemoglobins of microorganisms, especially of bacteria, and update several earlier and more comprehensive reviews, emphasising advances over the past 5 to 10 years and some controversies that have arisen. Inevitably, in light of space restrictions, details of nitric oxide metabolism and globins in higher organisms are brief.
Collapse
Affiliation(s)
- Robert K. Poole
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Sheffield, S10 2TN, UK
| |
Collapse
|
27
|
Daane JM, Giordano D, Coppola D, di Prisco G, Detrich HW, Verde C. Adaptations to environmental change: Globin superfamily evolution in Antarctic fishes. Mar Genomics 2019; 49:100724. [PMID: 31735579 DOI: 10.1016/j.margen.2019.100724] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 10/27/2019] [Accepted: 11/01/2019] [Indexed: 02/08/2023]
Abstract
The ancient origins and functional versatility of globins make them ideal subjects for studying physiological adaptation to environmental change. Our goals in this review are to describe the evolution of the vertebrate globin gene superfamily and to explore the structure/function relationships of hemoglobin, myoglobin, neuroglobin and cytoglobin in teleost fishes. We focus on the globins of Antarctic notothenioids, emphasizing their adaptive features as inferred from comparisons with human proteins. We dedicate this review to Guido di Prisco, our co-author, colleague, friend, and husband of C.V. Ever thoughtful, creative, and enthusiastic, Guido spearheaded study of the structure, function, and evolution of the hemoglobins of polar fishes - this review is testimony to his wide-ranging contributions. Throughout his career, Guido inspired younger scientists to embrace polar biological research, and he challenged researchers of all ages to explore evolutionary adaptation in the context of global climate change. Beyond his scientific contributions, we will miss his warmth, his culture, and his great intellect. Guido has left an outstanding legacy, one that will continue to inspire us and our research.
Collapse
Affiliation(s)
- Jacob M Daane
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, MA 01908, USA
| | - Daniela Giordano
- Institute of Biosciences and BioResources (IBBR), CNR, Via Pietro Castellino 111, 80131 Napoli, Italy; Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Daniela Coppola
- Institute of Biosciences and BioResources (IBBR), CNR, Via Pietro Castellino 111, 80131 Napoli, Italy; Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Guido di Prisco
- Institute of Biosciences and BioResources (IBBR), CNR, Via Pietro Castellino 111, 80131 Napoli, Italy
| | - H William Detrich
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, MA 01908, USA
| | - Cinzia Verde
- Institute of Biosciences and BioResources (IBBR), CNR, Via Pietro Castellino 111, 80131 Napoli, Italy; Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy.
| |
Collapse
|
28
|
Nye DB, Johnson EA, Mai MH, Lecomte JTJ. Replacement of the heme axial lysine as a test of conformational adaptability in the truncated hemoglobin THB1. J Inorg Biochem 2019; 201:110824. [PMID: 31514090 DOI: 10.1016/j.jinorgbio.2019.110824] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 09/03/2019] [Accepted: 09/03/2019] [Indexed: 10/26/2022]
Abstract
Amino acid replacement is a useful strategy to assess the roles of axial heme ligands in the function of native heme proteins. THB1, the protein product of the Chlamydomonas reinhardtii THB1 gene, is a group 1 truncated hemoglobin that uses a lysine residue in the E helix (Lys53, at position E10 by reference to myoglobin) as an iron ligand at neutral pH. Phylogenetic evidence shows that many homologous proteins have a histidine, methionine or arginine at the same position. In THB1, these amino acids would each be expected to convey distinct reactive properties if replacing the native lysine as an axial ligand. To explore the ability of the group 1 truncated Hb fold to support alternative ligation schemes and distal pocket conformations, the properties of the THB1 variants K53A as a control, K53H, K53M, and K53R were investigated by electronic absorption, EPR, and NMR spectroscopies. We found that His53 is capable of heme ligation in both the Fe(III) and Fe(II) states, that Met53 can coordinate only in the Fe(II) state, and that Arg53 stabilizes a hydroxide ligand in the Fe(III) state. The data illustrate that the group 1 truncated Hb fold can tolerate diverse rearrangement of the heme environment and has a strong tendency to use two protein side chains as iron ligands despite accompanying structural perturbations. Access to various redox pairs and different responses to pH make this protein an excellent test case for energetic and dynamic studies of heme ligation.
Collapse
Affiliation(s)
- Dillon B Nye
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Eric A Johnson
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Melissa H Mai
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Juliette T J Lecomte
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA.
| |
Collapse
|
29
|
Rivera S, Young PG, Hoffer ED, Vansuch GE, Metzler CL, Dunham CM, Weinert EE. Structural Insights into Oxygen-Dependent Signal Transduction within Globin Coupled Sensors. Inorg Chem 2018; 57:14386-14395. [PMID: 30378421 DOI: 10.1021/acs.inorgchem.8b02584] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In order to respond to external stimuli, bacteria have evolved sensor proteins linking external signals to intracellular outputs that can then regulate downstream pathways and phenotypes. Globin coupled sensor proteins (GCSs) serve to link environmental O2 levels to cellular processes by coupling a heme-containing sensor globin domain to a catalytic output domain. However, the mechanism by which O2 binding activates these proteins is currently unknown. To provide insights into the signaling mechanism, two distinct dimeric complexes of the isolated globin domain of the GCS from Bordetella pertussis ( BpeGlobin) were solved via X-ray crystallography in which differences in ligand-bound states were observed. Both monomers of one dimer contain Fe(II)-O2 states, while the other dimer consists of the Fe(III)-H2O and Fe(II)-O2 states. These data provide the first molecular insights into the heme pocket conformation of the active Fe(II)-O2 form of these enzymes. In addition, heme distortion modes and heme-protein interactions were found to correlate with the ligation state of the globin, suggesting that these conformational changes play a role in O2-dependent signaling. Fourier transform infrared spectroscopy (FTIR) of the full-length GCS from B. pertussis ( BpeGReg) and the closely related GCS from Pectobacterium carotovorum ssp. carotovorum ( PccGCS) confirmed the importance of an ordered water within the heme pocket and two distal residues (Tyr43 and Ser68) as hydrogen-bond donors. Taken together, this work provides mechanistic insights into BpeGReg O2 sensing and the signaling mechanisms of diguanylate cyclase-containing GCS proteins.
Collapse
Affiliation(s)
- Shannon Rivera
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Paul G Young
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Eric D Hoffer
- Department of Biochemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Gregory E Vansuch
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Carmen L Metzler
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Christine M Dunham
- Department of Biochemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Emily E Weinert
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| |
Collapse
|
30
|
Nye DB, Lecomte JTJ. Replacement of the Distal Histidine Reveals a Noncanonical Heme Binding Site in a 2-on-2 Hemoglobin. Biochemistry 2018; 57:5785-5796. [PMID: 30213188 PMCID: PMC6217817 DOI: 10.1021/acs.biochem.8b00752] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Heme ligation in hemoglobin is typically assumed by the "proximal" histidine. Hydrophobic contacts, ionic interactions, and the ligation bond secure the heme between two α-helices denoted E and F. Across the hemoglobin superfamily, several proteins also use a "distal" histidine, making the native state a bis-histidine complex. The group 1 truncated hemoglobin from Synechocystis sp. PCC 6803, GlbN, is one such bis-histidine protein. Ferric GlbN, in which the distal histidine (His46 or E10) has been replaced with a leucine, though expected to bind a water molecule and yield a high-spin iron complex at neutral pH, has low-spin spectral properties. Here, we applied nuclear magnetic resonance and electronic absorption spectroscopic methods to GlbN modified with heme and amino acid replacements to identify the distal ligand in H46L GlbN. We found that His117, a residue located in the C-terminal portion of the protein and on the proximal side of the heme, is responsible for the formation of an alternative bis-histidine complex. Simultaneous coordination by His70 and His117 situates the heme in a binding site different from the canonical site. This new holoprotein form is achieved with only local conformational changes. Heme affinity in the alternative site is weaker than in the normal site, likely because of strained coordination and a reduced number of specific heme-protein interactions. The observation of an unconventional heme binding site has important implications for the interpretation of mutagenesis results and globin homology modeling.
Collapse
Affiliation(s)
- Dillon B. Nye
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, United States
| | - Juliette T. J. Lecomte
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, United States
| |
Collapse
|
31
|
Bretl DJ, Ladd KM, Atkinson SN, Müller S, Kirby JR. Suppressor mutations reveal an NtrC-like response regulator, NmpR, for modulation of Type-IV Pili-dependent motility in Myxococcus xanthus. PLoS Genet 2018; 14:e1007714. [PMID: 30346960 PMCID: PMC6211767 DOI: 10.1371/journal.pgen.1007714] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 11/01/2018] [Accepted: 09/26/2018] [Indexed: 12/03/2022] Open
Abstract
Two-component signaling systems (TCS) regulate bacterial responses to environmental signals through the process of protein phosphorylation. Specifically, sensor histidine kinases (SK) recognize signals and propagate the response via phosphorylation of a cognate response regulator (RR) that functions to initiate transcription of specific genes. Signaling within a single TCS is remarkably specific and cross-talk between TCS is limited. However, regulation of the flow of information through complex signaling networks that include closely related TCS remains largely unknown. Additionally, many bacteria utilize multi-component signaling networks which provide additional genetic and biochemical interactions that must be regulated for signaling fidelity, input and output specificity, and phosphorylation kinetics. Here we describe the characterization of an NtrC-like RR that participates in regulation of Type-IV pilus-dependent motility of Myxococcus xanthus and is thus named NmpR, NtrC Modulator of Pili Regulator. A complex multi-component signaling system including NmpR was revealed by suppressor mutations that restored motility to cells lacking PilR, an evolutionarily conserved RR required for expression of pilA encoding the major Type-IV pilus monomer found in many bacterial species. The system contains at least four signaling proteins: a SK with a protoglobin sensor domain (NmpU), a hybrid SK (NmpS), a phospho-sink protein (NmpT), and an NtrC-like RR (NmpR). We demonstrate that ΔpilR bypass suppressor mutations affect regulation of the NmpRSTU multi-component system, such that NmpR activation is capable of restoring expression of pilA in the absence of PilR. Our findings indicate that pilus gene expression in M. xanthus is regulated by an extended network of TCS which interact to refine control of pilus function.
Collapse
Affiliation(s)
- Daniel J. Bretl
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States of America
| | - Kayla M. Ladd
- Department of Biochemistry, University of Iowa, Iowa City, Iowa, United States of America
| | - Samantha N. Atkinson
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States of America
- Department of Bioinformatics, University of Iowa, Iowa City, Iowa, United States of America
| | - Susanne Müller
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States of America
| | - John R. Kirby
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States of America
| |
Collapse
|
32
|
Johnson EA, Russo MM, Nye DB, Schlessman JL, Lecomte JTJ. Lysine as a heme iron ligand: A property common to three truncated hemoglobins from Chlamydomonas reinhardtii. Biochim Biophys Acta Gen Subj 2018; 1862:2660-2673. [PMID: 30251657 DOI: 10.1016/j.bbagen.2018.08.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 08/06/2018] [Accepted: 08/08/2018] [Indexed: 12/20/2022]
Abstract
BACKGROUND The nuclear genome of Chlamydomonas reinhardtii encodes a dozen hemoglobins of the truncated lineage. Four of these, named THB1-4, contain a single ~130-residue globin unit. THB1, which is cytoplasmic and capable of nitric oxide dioxygenation activity, uses a histidine and a lysine as axial ligands to the heme iron. In the present report, we compared THB2, THB3, and THB4 to THB1 to gain structural and functional insights into algal globins. METHODS We inspected properties of the globin domains prepared by recombinant means through site-directed mutagenesis, electronic absorption, CD, and NMR spectroscopies, and X-ray crystallography. RESULTS Recombinant THB3, which lacks the proximal histidine but has a distal histidine, binds heme weakly. NMR data demonstrate that the recombinant domains of THB2 and THB4 coordinate the ferrous heme iron with the proximal histidine and a lysine from the distal helix. An X-ray structure of ferric THB4 confirms lysine coordination. THB1, THB2, and THB4 have reduction potentials between -65 and -100 mV, are capable of nitric oxide dioxygenation, are reduced at different rates by the diaphorase domain of C. reinhardtii nitrate reductase, and show different response to peroxide treatment. CONCLUSIONS Three single-domain C. reinhardtii hemoglobins use lysine as a distal heme ligand in both Fe(III) and Fe(II) oxidation states. This common feature is likely related to enzymatic activity in the management of reactive oxygen species. GENERAL SIGNIFICANCE Primary structure analysis of hemoglobins has limited power in the prediction of heme ligation. Experimental determination reveals variations in this essential property across the superfamily.
Collapse
Affiliation(s)
- Eric A Johnson
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, United States
| | - Miranda M Russo
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, United States
| | - Dillon B Nye
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, United States
| | - Jamie L Schlessman
- Chemistry Department, U.S. Naval Academy, Annapolis, MD 21402, United States
| | - Juliette T J Lecomte
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, United States.
| |
Collapse
|
33
|
Feis A, Howes BD, Milazzo L, Coppola D, Smulevich G. Structural determinants of ligand binding in truncated hemoglobins: Resonance Raman spectroscopy of the native states and their carbon monoxide and hydroxide complexes. Biopolymers 2018; 109:e23114. [DOI: 10.1002/bip.23114] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 02/20/2018] [Accepted: 02/21/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Alessandro Feis
- Dipartimento di Chimica “Ugo Schiff,”; Università di Firenze, Via della Lastruccia 3-13; Sesto Fiorentino 50019 Italy
| | - Barry D. Howes
- Dipartimento di Chimica “Ugo Schiff,”; Università di Firenze, Via della Lastruccia 3-13; Sesto Fiorentino 50019 Italy
| | - Lisa Milazzo
- Dipartimento di Chimica “Ugo Schiff,”; Università di Firenze, Via della Lastruccia 3-13; Sesto Fiorentino 50019 Italy
| | - Daniela Coppola
- Dipartimento di Scienze bio-agroalimentari del CNR (DiSBA-CNR), CNR, Via Pietro Castellino 111; Naples I-80131 Italy
| | - Giulietta Smulevich
- Dipartimento di Chimica “Ugo Schiff,”; Università di Firenze, Via della Lastruccia 3-13; Sesto Fiorentino 50019 Italy
| |
Collapse
|
34
|
Coexistence of multiple globin genes conferring protection against nitrosative stress to the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125. Nitric Oxide 2018; 73:39-51. [DOI: 10.1016/j.niox.2017.12.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 12/07/2017] [Accepted: 12/18/2017] [Indexed: 11/20/2022]
|
35
|
Gallagher MD, Macqueen DJ. Evolution and Expression of Tissue Globins in Ray-Finned Fishes. Genome Biol Evol 2018; 9:32-47. [PMID: 28173090 PMCID: PMC5381549 DOI: 10.1093/gbe/evw266] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2016] [Indexed: 12/30/2022] Open
Abstract
The globin gene family encodes oxygen-binding hemeproteins conserved across the major branches of multicellular life. The origins and evolutionary histories of complete globin repertoires have been established for many vertebrates, but there remain major knowledge gaps for ray-finned fish. Therefore, we used phylogenetic, comparative genomic and gene expression analyses to discover and characterize canonical “non-blood” globin family members (i.e., myoglobin, cytoglobin, neuroglobin, globin-X, and globin-Y) across multiple ray-finned fish lineages, revealing novel gene duplicates (paralogs) conserved from whole genome duplication (WGD) and small-scale duplication events. Our key findings were that: (1) globin-X paralogs in teleosts have been retained from the teleost-specific WGD, (2) functional paralogs of cytoglobin, neuroglobin, and globin-X, but not myoglobin, have been conserved from the salmonid-specific WGD, (3) triplicate lineage-specific myoglobin paralogs are conserved in arowanas (Osteoglossiformes), which arose by tandem duplication and diverged under positive selection, (4) globin-Y is retained in multiple early branching fish lineages that diverged before teleosts, and (5) marked variation in tissue-specific expression of globin gene repertoires exists across ray-finned fish evolution, including several previously uncharacterized sites of expression. In this respect, our data provide an interesting link between myoglobin expression and the evolution of air breathing in teleosts. Together, our findings demonstrate great-unrecognized diversity in the repertoire and expression of nonblood globins that has arisen during ray-finned fish evolution.
Collapse
Affiliation(s)
- Michael D Gallagher
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Daniel J Macqueen
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
| |
Collapse
|
36
|
Bracke A, Hoogewijs D, Dewilde S. Exploring three different expression systems for recombinant expression of globins: Escherichia coli, Pichia pastoris and Spodoptera frugiperda. Anal Biochem 2017; 543:62-70. [PMID: 29203135 DOI: 10.1016/j.ab.2017.11.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 11/29/2017] [Accepted: 11/30/2017] [Indexed: 12/17/2022]
Abstract
Globins are among the best investigated proteins in biological and medical sciences and represent a prime tool for the study of the evolution of genes and the structure-function relationship of proteins. Here, we explore the recombinant expression of globins in three different expression systems: Escherichia coli, Pichia pastoris and the baculovirus infected Spodoptera frugiperda. We expressed two different human globin types in these three expression systems: I) the well-characterized neuroglobin and II) the uncharacterized, circular permutated globin domain of the large chimeric globin androglobin. It is clear from the literature that E.coli is the most used expression system for expression and purification of recombinant globins. However, the major disadvantage of E. coli is the formation of insoluble aggregates. We experienced that, for more complex multi-domain globins, like the chimeric globin androglobin, it is recommended to switch to a higher eukaryotic expression system.
Collapse
Affiliation(s)
- An Bracke
- Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, Antwerp 2610, Belgium
| | - David Hoogewijs
- Department of Medicine/Physiology, University of Fribourg, Chemin du Musée 5, CH 1700 Fribourg, Switzerland
| | - Sylvia Dewilde
- Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, Antwerp 2610, Belgium.
| |
Collapse
|
37
|
Gell DA. Structure and function of haemoglobins. Blood Cells Mol Dis 2017; 70:13-42. [PMID: 29126700 DOI: 10.1016/j.bcmd.2017.10.006] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 10/29/2017] [Accepted: 10/30/2017] [Indexed: 12/18/2022]
Abstract
Haemoglobin (Hb) is widely known as the iron-containing protein in blood that is essential for O2 transport in mammals. Less widely recognised is that erythrocyte Hb belongs to a large family of Hb proteins with members distributed across all three domains of life-bacteria, archaea and eukaryotes. This review, aimed chiefly at researchers new to the field, attempts a broad overview of the diversity, and common features, in Hb structure and function. Topics include structural and functional classification of Hbs; principles of O2 binding affinity and selectivity between O2/NO/CO and other small ligands; hexacoordinate (containing bis-imidazole coordinated haem) Hbs; bacterial truncated Hbs; flavohaemoglobins; enzymatic reactions of Hbs with bioactive gases, particularly NO, and protection from nitrosative stress; and, sensor Hbs. A final section sketches the evolution of work on the structural basis for allosteric O2 binding by mammalian RBC Hb, including the development of newer kinetic models. Where possible, reference to historical works is included, in order to provide context for current advances in Hb research.
Collapse
Affiliation(s)
- David A Gell
- School of Medicine, University of Tasmania, TAS 7000, Australia.
| |
Collapse
|
38
|
Van Doorslaer S, Cuypers B. Electron paramagnetic resonance of globin proteins – a successful match between spectroscopic development and protein research. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1392629] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
| | - Bert Cuypers
- Department of Physics, University of Antwerp, Antwerp, Belgium
| |
Collapse
|
39
|
Carabet LA, Guertin M, Lagüe P, Lamoureux G. Mechanism of the Nitric Oxide Dioxygenase Reaction of Mycobacterium tuberculosis Hemoglobin N. J Phys Chem B 2017; 121:8706-8718. [DOI: 10.1021/acs.jpcb.7b06494] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Lavinia A. Carabet
- Department of Chemistry
and Biochemistry and Centre for Research in Molecular
Modeling (CERMM), Concordia University, Montréal, Québec, Canada H4B 1R6
| | | | | | - Guillaume Lamoureux
- Department of Chemistry
and Biochemistry and Centre for Research in Molecular
Modeling (CERMM), Concordia University, Montréal, Québec, Canada H4B 1R6
| |
Collapse
|
40
|
Nitrosative stress defences of the enterohepatic pathogenic bacterium Helicobacter pullorum. Sci Rep 2017; 7:9909. [PMID: 28855660 PMCID: PMC5577044 DOI: 10.1038/s41598-017-10375-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 08/07/2017] [Indexed: 01/28/2023] Open
Abstract
Helicobacter pullorum is an avian bacterium that causes gastroenteritis, intestinal bowel and hepatobiliary diseases in humans. Although H. pullorum has been shown to activate the mammalian innate immunity with release of nitric oxide (NO), the proteins that afford protection against NO and reactive nitrogen species (RNS) remain unknown. Here several protein candidates of H. pullorum, namely a truncated (TrHb) and a single domain haemoglobin (SdHb), and three peroxiredoxin-like proteins (Prx1, Prx2 and Prx3) were investigated. We report that the two haemoglobin genes are induced by RNS, and that SdHb confers resistance to nitrosative stress both in vitro and in macrophages. For peroxiredoxins, the prx2 and prx3 expression is enhanced by peroxynitrite and hydrogen peroxide, respectively. Mutation of prx1 does not alter the resistance to these stresses, while the single ∆prx2 and double ∆prx1∆prx2 mutants have decreased viability. To corroborate the physiological data, the biochemical analysis of the five recombinant enzymes was done, namely by stopped-flow spectrophotometry. It is shown that H. pullorum SdHb reacts with NO much more quickly than TrHb, and that the three Prxs react promptly with peroxynitrite, Prx3 displaying the highest reactivity. Altogether, the results unveil SdHb and Prx3 as major protective systems of H. pullorum against nitrosative stress.
Collapse
|
41
|
Burns JL, Jariwala PB, Rivera S, Fontaine BM, Briggs L, Weinert EE. Oxygen-Dependent Globin Coupled Sensor Signaling Modulates Motility and Virulence of the Plant Pathogen Pectobacterium carotovorum. ACS Chem Biol 2017; 12:2070-2077. [PMID: 28612602 DOI: 10.1021/acschembio.7b00380] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Bacterial pathogens utilize numerous signals to identify the presence of their host and coordinate changes in gene expression that allow for infection. Within plant pathogens, these signals typically include small molecules and/or proteins from their plant hosts and bacterial quorum sensing molecules to ensure sufficient bacterial cell density for successful infection. In addition, bacteria use environmental signals to identify conditions when the host defenses are weakened and potentially to signal entry into an appropriate host/niche for infection. A globin coupled sensor protein (GCS), termed PccGCS, within the soft rot bacterium Pectobacterium carotovorum ssp. carotovorum WPP14 has been identified as an O2 sensor and demonstrated to alter virulence factor excretion and control motility, with deletion of PccGCS resulting in decreased rotting of a potato host. Using small molecules that modulate bacterial growth and quorum sensing, PccGCS signaling also has been shown to modulate quorum sensing pathways, resulting in the PccGCS deletion strain being more sensitive to plant-derived phenolic acids, which can function as quorum sensing inhibitors, and exhibiting increased N-acylhomoserine lactone (AHL) production. These findings highlight a role for GCS proteins in controlling key O2-dependent phenotypes of pathogenic bacteria and suggest that modulating GCS signaling to limit P. carotovorum motility may provide a means to decrease rotting of plant hosts.
Collapse
Affiliation(s)
- Justin L. Burns
- Department of Chemistry, Emory University, 1515
Dickey Drive, Atlanta, Georgia 30322, United States
| | - Parth B. Jariwala
- Department of Chemistry, Emory University, 1515
Dickey Drive, Atlanta, Georgia 30322, United States
| | - Shannon Rivera
- Department of Chemistry, Emory University, 1515
Dickey Drive, Atlanta, Georgia 30322, United States
| | - Benjamin M. Fontaine
- Department of Chemistry, Emory University, 1515
Dickey Drive, Atlanta, Georgia 30322, United States
| | - Laura Briggs
- Department of Chemistry, Emory University, 1515
Dickey Drive, Atlanta, Georgia 30322, United States
| | - Emily E. Weinert
- Department of Chemistry, Emory University, 1515
Dickey Drive, Atlanta, Georgia 30322, United States
| |
Collapse
|
42
|
Abstract
The discovery of the globin-coupled sensor (GCS) family of haem proteins has provided new insights into signalling proteins and pathways by which organisms sense and respond to changing oxygen levels. GCS proteins consist of a sensor globin domain linked to a variety of output domains, suggesting roles in controlling numerous cellular pathways, and behaviours in response to changing oxygen concentration. Members of this family of proteins have been identified in the genomes of numerous organisms and characterization of GCS with output domains, including methyl accepting chemotaxis proteins, kinases, and diguanylate cyclases, have yielded an understanding of the mechanism by which oxygen controls activity of GCS protein output domains, as well as downstream proteins and pathways regulated by GCS signalling. Future studies will expand our understanding of these proteins both in vitro and in vivo, likely demonstrating broad roles for GCS in controlling oxygen-dependent microbial physiology and phenotypes.
Collapse
|
43
|
Preimesberger MR, Majumdar A, Lecomte JTJ. Dynamics of Lysine as a Heme Axial Ligand: NMR Analysis of the Chlamydomonas reinhardtii Hemoglobin THB1. Biochemistry 2017; 56:551-569. [DOI: 10.1021/acs.biochem.6b00926] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Matthew R. Preimesberger
- T.
C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Ananya Majumdar
- Biomolecular
NMR Center, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Juliette T. J. Lecomte
- T.
C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
| |
Collapse
|
44
|
Uppal S, Singh AK, Arya R, Tewari D, Jaiswal N, Kapoor A, Bera AK, Nag A, Kundu S. Phe28 B10 Induces Channel-Forming Cytotoxic Amyloid Fibrillation in Human Neuroglobin, the Brain-Specific Hemoglobin. Biochemistry 2016; 55:6832-6847. [PMID: 27951646 DOI: 10.1021/acs.biochem.6b00617] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Since its discovery, neuroglobin (Ngb), a neuron-specific oxygen binding hemoglobin, distinct from the classical myoglobin and blood hemoglobin, has attracted attention as an endogenous neuroprotectant. Recent reports suggest that Ngb protects neurons from brain stroke, ischemic stress-induced degeneration, and other brain disorders. Proteins with a specific role in neuroprotection are often associated with neurodegeneration, as well, depending on the cellular environment or specific cellular triggers that tilt the balance one way or the other. This investigation explored the potential role of Ngb in amyloid fibril-related neuronal disorder. Ngb was capable of amyloid formation in vitro at neutral pH and ambient temperature, in both apo and holo forms, albeit at a slower rate in the holo form, unlike other hemoglobins that exhibit such behavior exclusively in the apo states. Elevated temperature enhanced the rate of fibril formation significantly. The B-helix, which is known to play a major role in Ngb ligand binding kinetics, was found to be amyloidogenic with the Phe28B10 amino acid side chain as the key inducer of fibrillation. The Ngb amyloid fibril was also significantly cytotoxic to neuroblastoma cell lines, compared to those obtained from reference hemoglobins. The Ngb fibril probably promoted toxicity by inducing channel formation in the cell membrane, as investigated here using synthetic lipid bilayer membranes and the propidium iodide uptake assay. These findings imply that Ngb plays a role in neurodegenerative disorders in vivo, for which there seems to be indirect evidence by association. Ngb thus presents a novel prospect for understanding amyloid-related brain disorders beyond the limited set of proteins currently investigated for such diseases.
Collapse
Affiliation(s)
- Sheetal Uppal
- Department of Biochemistry, University of Delhi South Campus , New Delhi 110021, India
| | - Amit Kumar Singh
- Department of Biochemistry, University of Delhi South Campus , New Delhi 110021, India
| | - Richa Arya
- Department of Biochemistry, University of Delhi South Campus , New Delhi 110021, India
| | - Debanjan Tewari
- Department of Biotechnology, Indian Institute of Technology Madras , Chennai 600036, India
| | - Neha Jaiswal
- Department of Biochemistry, University of Delhi South Campus , New Delhi 110021, India
| | - Abhijeet Kapoor
- Department of Biochemistry, University of Delhi South Campus , New Delhi 110021, India
| | - Amal Kanti Bera
- Department of Biotechnology, Indian Institute of Technology Madras , Chennai 600036, India
| | - Alo Nag
- Department of Biochemistry, University of Delhi South Campus , New Delhi 110021, India
| | - Suman Kundu
- Department of Biochemistry, University of Delhi South Campus , New Delhi 110021, India
| |
Collapse
|
45
|
Ascenzi P, di Masi A, Leboffe L, Fiocchetti M, Nuzzo MT, Brunori M, Marino M. Neuroglobin: From structure to function in health and disease. Mol Aspects Med 2016; 52:1-48. [DOI: 10.1016/j.mam.2016.10.004] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 10/27/2016] [Accepted: 10/27/2016] [Indexed: 01/01/2023]
|
46
|
Burns JL, Rivera S, Deer DD, Joynt SC, Dvorak D, Weinert EE. Oxygen and Bis(3',5')-cyclic Dimeric Guanosine Monophosphate Binding Control Oligomerization State Equilibria of Diguanylate Cyclase-Containing Globin Coupled Sensors. Biochemistry 2016; 55:6642-6651. [PMID: 27933792 DOI: 10.1021/acs.biochem.6b00526] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacteria sense their environment to alter phenotypes, including biofilm formation, to survive changing conditions. Heme proteins play important roles in sensing the bacterial gaseous environment and controlling the switch between motile and sessile (biofilm) states. Globin coupled sensors (GCS), a family of heme proteins consisting of a globin domain linked by a central domain to an output domain, are often found with diguanylate cyclase output domains that synthesize c-di-GMP, a major regulator of biofilm formation. Characterization of diguanylate cyclase-containing GCS proteins from Bordetella pertussis and Pectobacterium carotovorum demonstrated that cyclase activity is controlled by ligand binding to the heme within the globin domain. Both O2 binding to the heme within the globin domain and c-di-GMP binding to a product-binding inhibitory site (I-site) within the cyclase domain control oligomerization states of the enzymes. Changes in oligomerization state caused by c-di-GMP binding to the I-site also affect O2 kinetics within the globin domain, suggesting that shifting the oligomer equilibrium leads to broad rearrangements throughout the protein. In addition, mutations within the I-site that eliminate product inhibition result in changes to the accessible oligomerization states and decreased catalytic activity. These studies provide insight into the mechanism by which ligand binding to the heme and I-site controls activity of GCS proteins and suggests a role for oligomerization-dependent activity in vivo.
Collapse
Affiliation(s)
- Justin L Burns
- Department of Chemistry, Emory University , 1515 Dickey Drive, Atlanta, Georgia 30307, United States
| | - Shannon Rivera
- Department of Chemistry, Emory University , 1515 Dickey Drive, Atlanta, Georgia 30307, United States
| | - D Douglas Deer
- Department of Chemistry, Emory University , 1515 Dickey Drive, Atlanta, Georgia 30307, United States
| | - Shawnna C Joynt
- Department of Chemistry, Emory University , 1515 Dickey Drive, Atlanta, Georgia 30307, United States
| | - David Dvorak
- Department of Chemistry, Emory University , 1515 Dickey Drive, Atlanta, Georgia 30307, United States
| | - Emily E Weinert
- Department of Chemistry, Emory University , 1515 Dickey Drive, Atlanta, Georgia 30307, United States
| |
Collapse
|
47
|
Penta- and hexa-coordinate ferric hemoglobins display distinct pH titration profiles measured by Soret peak shifts. Anal Biochem 2016; 510:120-128. [DOI: 10.1016/j.ab.2016.07.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 06/14/2016] [Accepted: 07/14/2016] [Indexed: 11/20/2022]
|
48
|
Rivera S, Burns JL, Vansuch GE, Chica B, Weinert EE. Globin domain interactions control heme pocket conformation and oligomerization of globin coupled sensors. J Inorg Biochem 2016; 164:70-76. [PMID: 27614715 DOI: 10.1016/j.jinorgbio.2016.08.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 08/24/2016] [Accepted: 08/26/2016] [Indexed: 12/24/2022]
Abstract
Globin coupled sensors (GCS) are O2-sensing proteins used by bacteria to monitor the surrounding gaseous environment. To investigate the biphasic O2 dissociation kinetics observed for full-length GCS proteins, isolated globin domains from Pectobacterium carotovorum ssp. carotovorum (PccGlobin), and Bordetella pertussis (BpeGlobin), have been characterized. PccGlobin is found to be dimeric, while BpeGlobin is monomeric, indicating key differences in the globin domain dimer interface. Through characterization of wild type globin domains and globin variants with mutations at the dimer interface and within the distal pocket, dimerization of the globin domain is demonstrated to correlate with biphasic dissociation kinetics. Furthermore, a distal pocket tyrosine is identified as the primary hydrogen bond donor, while a secondary hydrogen bond donor within the distal heme pocket is involved in conformation(s) that lead to the second O2 dissociation rate. These findings highlight the role of the globin dimer interface in controlling properties of both the heme pocket and full-length GCS proteins.
Collapse
Affiliation(s)
- Shannon Rivera
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322 USA
| | - Justin L Burns
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322 USA
| | - Gregory E Vansuch
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322 USA
| | - Bryant Chica
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322 USA
| | - Emily E Weinert
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322 USA.
| |
Collapse
|
49
|
Abstract
If life without heme-Fe were at all possible, it would definitely be different. Indeed this complex and versatile iron-porphyrin macrocycle upon binding to different “globins” yields hemeproteins crucial to sustain a variety of vital functions, generally classified, for convenience, in a limited number of functional families. Over-and-above the array of functions briefly outlined below, the spectacular progress in molecular genetics seen over the last 30 years led to the discovery of many hitherto unknown novel hemeproteins in prokaryotes and eukaryotes. Here, we highlight a few basic aspects of the chemistry of the hemeprotein universe, in particular those that are relevant to the control of heme-Fe reactivity and specialization, as sculpted by a variety of interactions with the protein moiety.
Collapse
Affiliation(s)
- Paolo Ascenzi
- Dipartimento di Scienze, Università Roma Tre, Viale Marconi 446, I-00146 Roma, Italy
| | - Maurizio Brunori
- Dipartimento di Scienze Biochimiche “Alessandro Rossi Fanelli” and Istituto Pasteur — Fondazione Cenci, Bolognetti, Sapienza Università di Roma, Piazzale Aldo Moro 5, I-00185 Roma, Italy
| |
Collapse
|
50
|
Bustamante JP, Radusky L, Boechi L, Estrin DA, ten Have A, Martí MA. Evolutionary and Functional Relationships in the Truncated Hemoglobin Family. PLoS Comput Biol 2016; 12:e1004701. [PMID: 26788940 PMCID: PMC4720485 DOI: 10.1371/journal.pcbi.1004701] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 12/10/2015] [Indexed: 12/21/2022] Open
Abstract
Predicting function from sequence is an important goal in current biological research, and although, broad functional assignment is possible when a protein is assigned to a family, predicting functional specificity with accuracy is not straightforward. If function is provided by key structural properties and the relevant properties can be computed using the sequence as the starting point, it should in principle be possible to predict function in detail. The truncated hemoglobin family presents an interesting benchmark study due to their ubiquity, sequence diversity in the context of a conserved fold and the number of characterized members. Their functions are tightly related to O2 affinity and reactivity, as determined by the association and dissociation rate constants, both of which can be predicted and analyzed using in-silico based tools. In the present work we have applied a strategy, which combines homology modeling with molecular based energy calculations, to predict and analyze function of all known truncated hemoglobins in an evolutionary context. Our results show that truncated hemoglobins present conserved family features, but that its structure is flexible enough to allow the switch from high to low affinity in a few evolutionary steps. Most proteins display moderate to high oxygen affinities and multiple ligand migration paths, which, besides some minor trends, show heterogeneous distributions throughout the phylogenetic tree, again suggesting fast functional adaptation. Our data not only deepens our comprehension of the structural basis governing ligand affinity, but they also highlight some interesting functional evolutionary trends.
Collapse
Affiliation(s)
- Juan P. Bustamante
- Departamento de Química Inorgánica, Analítica y Química Física, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Leandro Radusky
- Departamento de Química Biológica e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Leonardo Boechi
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Darío A. Estrin
- Departamento de Química Inorgánica, Analítica y Química Física, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Arjen ten Have
- Instituto de Investigación Biológica, CONICET, Universidad Nacional de Mar del Plata. Buenos Aires, Argentina
| | - Marcelo A. Martí
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| |
Collapse
|