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Sinha PR, Balasubramanian R, Hegde SR. Integrated sequence and -omic features reveal novel small proteome of Mycobacterium tuberculosis. Front Microbiol 2024; 15:1335310. [PMID: 38812687 PMCID: PMC11133741 DOI: 10.3389/fmicb.2024.1335310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 04/15/2024] [Indexed: 05/31/2024] Open
Abstract
Bioinformatic studies on small proteins are under-represented due to difficulties in annotation posed by their small size. However, recent discoveries emphasize the functional significance of small proteins in cellular processes including cell signaling, metabolism, and adaptation to stress. In this study, we utilized a Random Forest classifier trained on sequence features, RNA-Seq, and Ribo-Seq data to uncover small proteins (smORFs) in M. tuberculosis. Independent predictions for the exponential and starvation conditions resulted in 695 potential smORFs. We examined the functional implications of these smORFs using homology searches, LC-MS/MS, and ChIP-seq data, testing their expression in diverse growth conditions, and identifying protein domains. We provide evidence that some of these smORFs could be part of operons, or exist as upstream ORFs. This expanded data resource for the proteins of M. tuberculosis would aid in fine-tuning the existing protein and gene regulatory networks, thereby improving system-wide studies. The primary goal of this study was to uncover and characterize smORFs in M. tuberculosis through bioinformatic analysis, shedding light on their functional roles and genomic organization. Further investigation of these potential smORFs would provide valuable insights into the genome organization and functional diversity of the M. tuberculosis proteome.
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Affiliation(s)
| | | | - Shubhada R. Hegde
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, India
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2
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Zuchowski R, Schito S, Neuheuser F, Menke P, Berger D, Hollmann N, Gujar S, Sundermeyer L, Mack C, Wirtz A, Weiergräber OH, Polen T, Bott M, Noack S, Baumgart M. Discovery of novel amino acid production traits by evolution of synthetic co-cultures. Microb Cell Fact 2023; 22:71. [PMID: 37061714 PMCID: PMC10105947 DOI: 10.1186/s12934-023-02078-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 04/02/2023] [Indexed: 04/17/2023] Open
Abstract
BACKGROUND Amino acid production features of Corynebacterium glutamicum were extensively studied in the last two decades. Many metabolic pathways, regulatory and transport principles are known, but purely rational approaches often provide only limited progress in production optimization. We recently generated stable synthetic co-cultures, termed Communities of Niche-optimized Strains (CoNoS), that rely on cross-feeding of amino acids for growth. This setup has the potential to evolve strains with improved production by selection of faster growing communities. RESULTS Here we performed adaptive laboratory evolution (ALE) with a CoNoS to identify mutations that are relevant for amino acid production both in mono- and co-cultures. During ALE with the CoNoS composed of strains auxotrophic for either L-leucine or L-arginine, we obtained a 23% growth rate increase. Via whole-genome sequencing and reverse engineering, we identified several mutations involved in amino acid transport that are beneficial for CoNoS growth. The L-leucine auxotrophic strain carried an expression-promoting mutation in the promoter region of brnQ (cg2537), encoding a branched-chain amino acid transporter in combination with mutations in the genes for the Na+/H+-antiporter Mrp1 (cg0326-cg0321). This suggested an unexpected link of Mrp1 to L-leucine transport. The L-arginine auxotrophic partner evolved expression-promoting mutations near the transcriptional start site of the yet uncharacterized operon argTUV (cg1504-02). By mutation studies and ITC, we characterized ArgTUV as the only L-arginine uptake system of C. glutamicum with an affinity of KD = 30 nM. Finally, deletion of argTUV in an L-arginine producer strain resulted in a faster and 24% higher L-arginine production in comparison to the parental strain. CONCLUSION Our work demonstrates the power of the CoNoS-approach for evolution-guided identification of non-obvious production traits, which can also advance amino acid production in monocultures. Further rounds of evolution with import-optimized strains can potentially reveal beneficial mutations also in metabolic pathway enzymes. The approach can easily be extended to all kinds of metabolite cross-feeding pairings of different organisms or different strains of the same organism, thereby enabling the identification of relevant transport systems and other favorable mutations.
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Affiliation(s)
- Rico Zuchowski
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Simone Schito
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Friederike Neuheuser
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Philipp Menke
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Daniel Berger
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Niels Hollmann
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Srushti Gujar
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
- Institute of Biological Information Processing, IBI-7: Structural Biochemistry, Forschungszentrum Jülich, Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Lea Sundermeyer
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Christina Mack
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Astrid Wirtz
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Oliver H Weiergräber
- Institute of Biological Information Processing, IBI-7: Structural Biochemistry, Forschungszentrum Jülich, Jülich, Germany
| | - Tino Polen
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Michael Bott
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Stephan Noack
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Meike Baumgart
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany.
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Parreira de Aquino G, Mendes Gomes MA, Köpke Salinas R, Laranjeira-Silva MF. Lipid and fatty acid metabolism in trypanosomatids. MICROBIAL CELL 2021; 8:262-275. [PMID: 34782859 PMCID: PMC8561143 DOI: 10.15698/mic2021.11.764] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 09/03/2021] [Accepted: 09/13/2021] [Indexed: 12/18/2022]
Abstract
Trypanosomiases and leishmaniases are neglected tropical diseases that have been spreading to previously non-affected areas in recent years. Identification of new chemotherapeutics is needed as there are no vaccines and the currently available treatment options are highly toxic and often ineffective. The causative agents for these diseases are the protozoan parasites of the Trypanosomatidae family, and they alternate between invertebrate and vertebrate hosts during their life cycles. Hence, these parasites must be able to adapt to different environments and compete with their hosts for several essential compounds, such as amino acids, vitamins, ions, carbohydrates, and lipids. Among these nutrients, lipids and fatty acids (FAs) are essential for parasite survival. Trypanosomatids require massive amounts of FAs, and they can either synthesize FAs de novo or scavenge them from the host. Moreover, FAs are the major energy source during specific life cycle stages of T. brucei, T. cruzi, and Leishmania. Therefore, considering the distinctive features of FAs metabolism in trypanosomatids, these pathways could be exploited for the development of novel antiparasitic drugs. In this review, we highlight specific aspects of lipid and FA metabolism in the protozoan parasites T. brucei, T. cruzi, and Leishmania spp., as well as the pathways that have been explored for the development of new chemotherapies.
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Affiliation(s)
| | | | - Roberto Köpke Salinas
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
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4
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Parada C, Neri-Badillo IC, Vallecillo AJ, Segura E, Silva-Miranda M, Guzmán-Gutiérrez SL, Ortega PA, Coronado-Aceves EW, Cancino-Villeda L, Torres-Larios A, Aceves Sánchez MDJ, Flores Valdez MA, Espitia C. New Insights into the Methylation of Mycobacterium tuberculosis Heparin Binding Hemagglutinin Adhesin Expressed in Rhodococcus erythropolis. Pathogens 2021; 10:pathogens10091139. [PMID: 34578171 PMCID: PMC8467707 DOI: 10.3390/pathogens10091139] [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: 07/18/2021] [Revised: 08/19/2021] [Accepted: 08/30/2021] [Indexed: 12/02/2022] Open
Abstract
In recent years, knowledge of the role that protein methylation is playing on the physiopathogenesis of bacteria has grown. In Mycobacterium tuberculosis, methylation of the heparin binding hemagglutinin adhesin modulates the immune response, making this protein a subunit vaccine candidate. Through its C-terminal lysine-rich domain, this surface antigen interacts with heparan sulfate proteoglycans present in non-phagocytic cells, leading to extrapulmonary dissemination of the pathogen. In this study, the adhesin was expressed as a recombinant methylated protein in Rhodococcus erythropolis L88 and it was found associated to lipid droplets when bacteria were grown under nitrogen limitation. In order to delve into the role methylation could have in host–pathogen interactions, a comparative analysis was carried out between methylated and unmethylated protein produced in Escherichia coli. We found that methylation had an impact on lowering protein isoelectric point, but no differences between the proteins were found in their capacity to interact with heparin and A549 epithelial cells. An important finding was that HbhA is a Fatty Acid Binding Protein and differences in the conformational stability of the protein in complex with the fatty acid were observed between methylated and unmethylated protein. Together, these results suggest that the described role for this mycobacteria protein in lipid bodies formation could be related to its capacity to transport fatty acids. Obtained results also provide new clues about the role HbhA methylation could have in tuberculosis and point out the importance of having heterologous expression systems to obtain modified proteins.
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Affiliation(s)
- Cristina Parada
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (C.P.); (I.C.N.-B.); (A.J.V.); (E.S.); (M.S.-M.); (S.L.G.-G.); (P.A.O.); (E.W.C.-A.); (L.C.-V.)
| | - Isabel Cecilia Neri-Badillo
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (C.P.); (I.C.N.-B.); (A.J.V.); (E.S.); (M.S.-M.); (S.L.G.-G.); (P.A.O.); (E.W.C.-A.); (L.C.-V.)
| | - Antonio J. Vallecillo
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (C.P.); (I.C.N.-B.); (A.J.V.); (E.S.); (M.S.-M.); (S.L.G.-G.); (P.A.O.); (E.W.C.-A.); (L.C.-V.)
- Facultad de Ciencias Agropecuarias, Universidad de Cuenca, Cuenca 010220, Ecuador
| | - Erika Segura
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (C.P.); (I.C.N.-B.); (A.J.V.); (E.S.); (M.S.-M.); (S.L.G.-G.); (P.A.O.); (E.W.C.-A.); (L.C.-V.)
| | - Mayra Silva-Miranda
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (C.P.); (I.C.N.-B.); (A.J.V.); (E.S.); (M.S.-M.); (S.L.G.-G.); (P.A.O.); (E.W.C.-A.); (L.C.-V.)
- Consejo Nacional de Ciencia y Tecnología, CONACyT, Ciudad de México 03940, Mexico
| | - Silvia Laura Guzmán-Gutiérrez
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (C.P.); (I.C.N.-B.); (A.J.V.); (E.S.); (M.S.-M.); (S.L.G.-G.); (P.A.O.); (E.W.C.-A.); (L.C.-V.)
- Consejo Nacional de Ciencia y Tecnología, CONACyT, Ciudad de México 03940, Mexico
| | - Paola A. Ortega
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (C.P.); (I.C.N.-B.); (A.J.V.); (E.S.); (M.S.-M.); (S.L.G.-G.); (P.A.O.); (E.W.C.-A.); (L.C.-V.)
| | - Enrique Wenceslao Coronado-Aceves
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (C.P.); (I.C.N.-B.); (A.J.V.); (E.S.); (M.S.-M.); (S.L.G.-G.); (P.A.O.); (E.W.C.-A.); (L.C.-V.)
| | - Laura Cancino-Villeda
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (C.P.); (I.C.N.-B.); (A.J.V.); (E.S.); (M.S.-M.); (S.L.G.-G.); (P.A.O.); (E.W.C.-A.); (L.C.-V.)
| | - Alfredo Torres-Larios
- Department of Biochemistry and Structural Biology, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico;
| | - Michel de Jesús Aceves Sánchez
- Biotecnología Médica y Farmacéutica, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C., Guadalajara 44270, Mexico; (M.d.J.A.S.); (M.A.F.V.)
| | - Mario Alberto Flores Valdez
- Biotecnología Médica y Farmacéutica, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C., Guadalajara 44270, Mexico; (M.d.J.A.S.); (M.A.F.V.)
| | - Clara Espitia
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (C.P.); (I.C.N.-B.); (A.J.V.); (E.S.); (M.S.-M.); (S.L.G.-G.); (P.A.O.); (E.W.C.-A.); (L.C.-V.)
- Correspondence:
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5
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Protocols and pitfalls in obtaining fatty acid-binding proteins for biophysical studies of ligand-protein and protein-protein interactions. Biochem Biophys Rep 2017; 10:318-324. [PMID: 28955759 PMCID: PMC5614677 DOI: 10.1016/j.bbrep.2017.05.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 04/26/2017] [Accepted: 05/03/2017] [Indexed: 01/22/2023] Open
Abstract
Adipocyte fatty acid-binding protein (AFABP: FABP4) is a member of the intracellular lipid-binding protein family that is thought to target long-chain fatty acids to nuclear receptors such as peroxisome proliferator-activated receptor gamma (PPARγ), which in turn plays roles in insulin resistance and obesity. A molecular understanding of AFABP function requires robust isolation of the protein in liganded and free forms as well as characterization of its oligomerization state(s) under physiological conditions. We report development of a protocol to optimize the production of members of this protein family in pure form, including removal of their bound lipids by mixing with hydrophobically functionalized hydroxypropyl dextran beads and validation by two-dimensional NMR spectroscopy. The formation of self-associated or covalently bonded protein dimers was evaluated critically using gel filtration chromatography, revealing conditions that promote or prevent formation of disulfide-linked homodimers. The resulting scheme provides a solid foundation for future investigations of AFABP interactions with key ligand and protein partners involved in lipid metabolism.
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Key Words
- AFABP, adipose fatty acid-binding protein
- Delipidation
- Disulfide bond
- ESI-MS, Electrospray Ionization Mass Spectrometry
- FABP, fatty acid-binding protein
- Fatty acid-binding protein
- GF, Gel filtration chromatography
- HSQC, [1H–15N] heteronuclear single quantum correlation spectroscopy
- Homodimer
- LCFA, Long-chain fatty acid
- Ligand
- MALDI-TOF, Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry
- NMR, Nuclear Magnetic Resonance
- NOESY, 2D nuclear Overhauser spectroscopy
- PPAR, peroxisome proliferator-activated receptor
- Protein
- TCEP, tris(2-carboxyethyl)phosphine
- TEV, Tobacco Etch Virus
- TOCSY, 2D Total correlation spectroscopy
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6
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Chandra G, Chater KF. Developmental biology of Streptomyces from the perspective of 100 actinobacterial genome sequences. FEMS Microbiol Rev 2014; 38:345-79. [PMID: 24164321 PMCID: PMC4255298 DOI: 10.1111/1574-6976.12047] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 08/06/2013] [Accepted: 08/20/2013] [Indexed: 12/22/2022] Open
Abstract
To illuminate the evolution and mechanisms of actinobacterial complexity, we evaluate the distribution and origins of known Streptomyces developmental genes and the developmental significance of actinobacteria-specific genes. As an aid, we developed the Actinoblast database of reciprocal blastp best hits between the Streptomyces coelicolor genome and more than 100 other actinobacterial genomes (http://streptomyces.org.uk/actinoblast/). We suggest that the emergence of morphological complexity was underpinned by special features of early actinobacteria, such as polar growth and the coupled participation of regulatory Wbl proteins and the redox-protecting thiol mycothiol in transducing a transient nitric oxide signal generated during physiologically stressful growth transitions. It seems that some cell growth and division proteins of early actinobacteria have acquired greater importance for sporulation of complex actinobacteria than for mycelial growth, in which septa are infrequent and not associated with complete cell separation. The acquisition of extracellular proteins with structural roles, a highly regulated extracellular protease cascade, and additional regulatory genes allowed early actinobacterial stationary phase processes to be redeployed in the emergence of aerial hyphae from mycelial mats and in the formation of spore chains. These extracellular proteins may have contributed to speciation. Simpler members of morphologically diverse clades have lost some developmental genes.
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Holler TP, Evdokimov AG, Narasimhan L. Structural biology approaches to antibacterial drug discovery. Expert Opin Drug Discov 2013; 2:1085-101. [PMID: 23484874 DOI: 10.1517/17460441.2.8.1085] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Antibacterial drug discovery has undertaken a major experiment in the 12 years since the first bacterial genomes were sequenced. Genome mining has identified hundreds of potential targets that have been distilled to a relatively small number of broad-spectrum targets ('low-hanging fruit') using the genetics tools of modern microbiology. Prosecuting these targets with high-throughput screens has led to a disappointingly small number of lead series that have mostly evaporated under closer scrutiny. In the meantime, multi-drug resistant pathogens are becoming a serious challenge in the clinic and the community and the number of pharmaceutical firms pursuing antibacterial discovery has declined. Filling the antibacterial development pipeline with novel chemical series is a significant challenge that will require the collaboration of scientists from many disciplines. Fortunately, advancements in the tools of structural biology and of in silico modeling are opening up new avenues of research that may help deal with the problems associated with discovering novel antibiotics.
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Affiliation(s)
- Tod P Holler
- Pfizer Global Research and Development, 2800 Plymouth Road, Ann Arbor, MI 48105, USA +1 734 622 5954 ; +1 734 622 2963 ; Tod.Holler@pfizer. com
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8
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Dávila Costa JS, Kothe E, Abate CM, Amoroso MJ. Unraveling the Amycolatopsis tucumanensis copper-resistome. Biometals 2012; 25:905-17. [DOI: 10.1007/s10534-012-9557-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Accepted: 05/01/2012] [Indexed: 01/07/2023]
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9
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Munaron L. Shuffling the cards in signal transduction: Calcium, arachidonic acid and mechanosensitivity. World J Biol Chem 2011; 2:59-66. [PMID: 21537474 PMCID: PMC3083947 DOI: 10.4331/wjbc.v2.i4.59] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Revised: 04/12/2011] [Accepted: 04/19/2011] [Indexed: 02/05/2023] Open
Abstract
Cell signaling is a very complex network of biochemical reactions triggered by a huge number of stimuli coming from the external medium. The function of any single signaling component depends not only on its own structure but also on its connections with other biomolecules. During prokaryotic-eukaryotic transition, the rearrangement of cell organization in terms of diffusional compartmentalization exerts a deep change in cell signaling functional potentiality. In this review I briefly introduce an intriguing ancient relationship between pathways involved in cell responses to chemical agonists (growth factors, nutrients, hormones) as well as to mechanical forces (stretch, osmotic changes). Some biomolecules (ion channels and enzymes) act as “hubs”, thanks to their ability to be directly or indirectly chemically/mechanically co-regulated. In particular calcium signaling machinery and arachidonic acid metabolism are very ancient networks, already present before eukaryotic appearance. A number of molecular “hubs”, including phospholipase A2 and some calcium channels, appear tightly interconnected in a cross regulation leading to the cellular response to chemical and mechanical stimulations.
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Affiliation(s)
- Luca Munaron
- Luca Munaron, Department of Animal and Human Biology, Nanostructured Interfaces and Surfaces Centre of Excellence, Center for Complex Systems in Molecular Biology and Medicine, University of Torino, 10123 Torino, Italy
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10
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Bianchetti CM, Bingman CA, Phillips GN. Structure of the C-terminal heme-binding domain of THAP domain containing protein 4 from Homo sapiens. Proteins 2011; 79:1337-41. [PMID: 21387410 PMCID: PMC3179982 DOI: 10.1002/prot.22944] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Accepted: 11/05/2010] [Indexed: 01/07/2023]
Affiliation(s)
- Christopher M. Bianchetti
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA,Centers for Eukaryotic Structural Genomics, University of Wisconsin, Madison, WI 53706, USA
| | - Craig A. Bingman
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA,Centers for Eukaryotic Structural Genomics, University of Wisconsin, Madison, WI 53706, USA
| | - George N. Phillips
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA,Centers for Eukaryotic Structural Genomics, University of Wisconsin, Madison, WI 53706, USA
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11
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Bianchetti CM, Blouin GC, Bitto E, Olson JS, Phillips GN. The structure and NO binding properties of the nitrophorin-like heme-binding protein from Arabidopsis thaliana gene locus At1g79260.1. Proteins 2010; 78:917-31. [PMID: 19938152 PMCID: PMC2811769 DOI: 10.1002/prot.22617] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The protein from Arabidopsis thaliana gene locus At1g79260.1 is comprised of 166-residues and is of previously unknown function. Initial structural studies by the Center for Eukaryotic Structural Genomics (CESG) suggested that this protein might bind heme, and consequently, the crystal structures of apo and heme-bound forms were solved to near atomic resolution of 1.32 A and 1.36 A, respectively. The rate of hemin loss from the protein was measured to be 3.6 x 10(-5) s(-1), demonstrating that it binds heme specifically and with high affinity. The protein forms a compact 10-stranded beta-barrel that is structurally similar to the lipocalins and fatty acid binding proteins (FABPs). One group of lipocalins, the nitrophorins (NP), are heme proteins involved in nitric oxide (NO) transport and show both sequence and structural similarity to the protein from At1g79260.1 and two human homologues, all of which contain a proximal histidine capable of coordinating a heme iron. Rapid-mixing and laser photolysis techniques were used to determine the rate constants for carbon monoxide (CO) binding to the ferrous form of the protein (k'(CO) = 0.23 microM(-1) s(-1), k(CO) = 0.050 s(-1)) and NO binding to the ferric form (k'(NO) = 1.2 microM(-1) s(-1), k(NO) = 73 s(-1)). Based on both structural and functional similarity to the nitrophorins, we have named the protein nitrobindin and hypothesized that it plays a role in NO transport. However, one of the two human homologs of nitrobindin contains a THAP domain, implying a possible role in apoptosis. Proteins 2010. (c) 2009 Wiley-Liss, Inc.
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Affiliation(s)
- Christopher M. Bianchetti
- Departments of Biochemistry, University of Wisconsin, Madison, WI 53706, USA,Centers for Eukaryotic Structural Genomics, University of Wisconsin, Madison, WI 53706, USA
| | - George C. Blouin
- Department of Biochemistry and Cell Biology and the W. M. Keck Center for Computational Biology, Rice University, Houston, Texas 77005
| | - Eduard Bitto
- Department of Chemistry and Biochemistry, Georgian Court University, Lakewood NJ 08701
| | - John S. Olson
- Department of Biochemistry and Cell Biology and the W. M. Keck Center for Computational Biology, Rice University, Houston, Texas 77005
| | - George N. Phillips
- Departments of Biochemistry, University of Wisconsin, Madison, WI 53706, USA,Centers for Eukaryotic Structural Genomics, University of Wisconsin, Madison, WI 53706, USA
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12
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Alvite G, Canclini L, Corvo I, Esteves A. Two novel Mesocestoides vogae fatty acid binding proteins - functional and evolutionary implications. FEBS J 2007; 275:107-16. [DOI: 10.1111/j.1742-4658.2007.06179.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Graña M, Haouz A, Buschiazzo A, Miras I, Wehenkel A, Bondet V, Shepard W, Schaeffer F, Cole ST, Alzari PM. The crystal structure of M. leprae ML2640c defines a large family of putative S-adenosylmethionine-dependent methyltransferases in mycobacteria. Protein Sci 2007; 16:1896-904. [PMID: 17660248 PMCID: PMC2206960 DOI: 10.1110/ps.072982707] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Mycobacterium leprae protein ML2640c belongs to a large family of conserved hypothetical proteins predominantly found in mycobacteria, some of them predicted as putative S-adenosylmethionine (AdoMet)-dependent methyltransferases (MTase). As part of a Structural Genomics initiative on conserved hypothetical proteins in pathogenic mycobacteria, we have determined the structure of ML2640c in two distinct crystal forms. As expected, ML2640c has a typical MTase core domain and binds the methyl donor substrate AdoMet in a manner consistent with other known members of this structural family. The putative acceptor substrate-binding site of ML2640c is a large internal cavity, mostly lined by aromatic and aliphatic side-chain residues, suggesting that a lipid-like molecule might be targeted for catalysis. A flap segment (residues 222-256), which isolates the binding site from the bulk solvent and is highly mobile in the crystal structures, could serve as a gateway to allow substrate entry and product release. The multiple sequence alignment of ML2640c-like proteins revealed that the central alpha/beta core and the AdoMet-binding site are very well conserved within the family. However, the amino acid positions defining the binding site for the acceptor substrate display a higher variability, suggestive of distinct acceptor substrate specificities. The ML2640c crystal structures offer the first structural glimpses at this important family of mycobacterial proteins and lend strong support to their functional assignment as AdoMet-dependent methyltransferases.
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Affiliation(s)
- Martin Graña
- Unité de Biochimie Structurale (CNRS-URA 2185), Institut Pasteur, 75724 Paris, France
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