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Manganese Detoxification by MntE Is Critical for Resistance to Oxidative Stress and Virulence of Staphylococcus aureus. mBio 2019; 10:mBio.02915-18. [PMID: 30808698 PMCID: PMC6391924 DOI: 10.1128/mbio.02915-18] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Manganese (Mn) is generally viewed as a critical nutrient that is beneficial to pathogenic bacteria due to its function as an enzymatic cofactor and its capability of acting as an antioxidant; yet paradoxically, high concentrations of this transition metal can be toxic. In this work, we demonstrate Staphylococcus aureus utilizes the cation diffusion facilitator (CDF) family protein MntE to alleviate Mn toxicity through efflux of excess Mn. Inactivation of mntE leads to a significant reduction in S. aureus resistance to oxidative stress and S. aureus-mediated mortality within a mouse model of systemic infection. These results highlight the importance of MntE-mediated Mn detoxification in intracellular Mn homeostasis, resistance to oxidative stress, and S. aureus virulence. Therefore, this establishes MntE as a potential target for development of anti-S. aureus therapeutics. Manganese (Mn) is an essential micronutrient critical for the pathogenesis of Staphylococcus aureus, a significant cause of human morbidity and mortality. Paradoxically, excess Mn is toxic; therefore, maintenance of intracellular Mn homeostasis is required for survival. Here we describe a Mn exporter in S. aureus, MntE, which is a member of the cation diffusion facilitator (CDF) protein family and conserved among Gram-positive pathogens. Upregulation of mntE transcription in response to excess Mn is dependent on the presence of MntR, a transcriptional repressor of the mntABC Mn uptake system. Inactivation of mntE or mntR leads to reduced growth in media supplemented with Mn, demonstrating MntE is required for detoxification of excess Mn. Inactivation of mntE results in elevated levels of intracellular Mn, but reduced intracellular iron (Fe) levels, supporting the hypothesis that MntE functions as a Mn efflux pump and Mn efflux influences Fe homeostasis. Strains inactivated for mntE are more sensitive to the oxidants NaOCl and paraquat, indicating Mn homeostasis is critical for resisting oxidative stress. Furthermore, mntE and mntR are required for full virulence of S. aureus during infection, suggesting S. aureus experiences Mn toxicity in vivo. Combined, these data support a model in which MntR controls Mn homeostasis by balancing transcriptional repression of mntABC and induction of mntE, both of which are critical for S. aureus pathogenesis. Thus, Mn efflux contributes to bacterial survival and virulence during infection, establishing MntE as a potential antimicrobial target and expanding our understanding of Mn homeostasis.
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102
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Yoshino K, Yamamoto K, Hara K, Sonoda M, Yamamoto Y, Sakamoto K. The conservation of polyol transporter proteins and their involvement in lichenized Ascomycota. Fungal Biol 2019; 123:318-329. [PMID: 30928040 DOI: 10.1016/j.funbio.2019.01.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 12/30/2018] [Accepted: 01/21/2019] [Indexed: 01/08/2023]
Abstract
In lichen symbiosis, polyol transfer from green algae is important for acquiring the fungal carbon source. However, the existence of polyol transporter genes and their correlation with lichenization remain unclear. Here, we report candidate polyol transporter genes selected from the genome of the lichen-forming fungus (LFF) Ramalina conduplicans. A phylogenetic analysis using characterized polyol and monosaccharide transporter proteins and hypothetical polyol transporter proteins of R. conduplicans and various ascomycetous fungi suggested that the characterized yeast' polyol transporters form multiple clades with the polyol transporter-like proteins selected from the diverse ascomycetous taxa. Thus, polyol transporter genes are widely conserved among Ascomycota, regardless of lichen-forming status. In addition, the phylogenetic clusters suggested that LFFs belonging to Lecanoromycetes have duplicated proteins in each cluster. Consequently, the number of sequences similar to characterized yeast' polyol transporters were evaluated using the genomes of 472 species or strains of Ascomycota. Among these, LFFs belonging to Lecanoromycetes had greater numbers of deduced polyol transporter proteins. Thus, various polyol transporters are conserved in Ascomycota and polyol transporter genes appear to have expanded during the evolution of Lecanoromycetes.
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Affiliation(s)
- Kanami Yoshino
- Division of Environmental Horticulture, Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-0092, Japan.
| | - Kohei Yamamoto
- Tochigi Prefectural Museum, 2-2 Mutsumi-cho, Utsunomiya, Tochigi, 320-0865, Japan.
| | - Kojiro Hara
- Faculty of Bioresource Sciences, Akita Prefectural University, 241-438 Kaidobata-nishi, Shimoshinjo-nakano, Akita, 010-0195, Japan.
| | - Masatoshi Sonoda
- Division of Environmental Horticulture, Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-0092, Japan.
| | - Yoshikazu Yamamoto
- Faculty of Bioresource Sciences, Akita Prefectural University, 241-438 Kaidobata-nishi, Shimoshinjo-nakano, Akita, 010-0195, Japan.
| | - Kazunori Sakamoto
- Division of Environmental Horticulture, Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-0092, Japan.
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103
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Colina-Tenorio L, Miranda-Astudillo H, Dautant A, Vázquez-Acevedo M, Giraud MF, González-Halphen D. Subunit Asa3 ensures the attachment of the peripheral stalk to the membrane sector of the dimeric ATP synthase of Polytomella sp. Biochem Biophys Res Commun 2018; 509:341-347. [PMID: 30585150 DOI: 10.1016/j.bbrc.2018.12.142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 12/19/2018] [Indexed: 02/04/2023]
Abstract
The mitochondrial ATP synthase of Polytomella exhibits a peripheral stalk and a dimerization domain built by the Asa subunits, unique to chlorophycean algae. The topology of these subunits has been extensively studied. Here we explored the interactions of subunit Asa3 using Far Western blotting and subcomplex reconstitution, and found it associates with Asa1 and Asa8. We also identified the novel interactions Asa1-Asa2 and Asa1-Asa7. In silico analyses of Asa3 revealed that it adopts a HEAT repeat-like structure that points to its location within the enzyme based on the available 3D-map of the algal ATP synthase. We suggest that subunit Asa3 is instrumental in securing the attachment of the peripheral stalk to the membrane sector, thus stabilizing the dimeric mitochondrial ATP synthase.
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Affiliation(s)
- Lilia Colina-Tenorio
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | | | - Alain Dautant
- CNRS, UMR5095, IBGC, Bordeaux, France; Energy Transducing Systems and Mitochondrial Morphology, Université de Bordeaux, Bordeaux, France
| | - Miriam Vázquez-Acevedo
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Marie-France Giraud
- CNRS, UMR5095, IBGC, Bordeaux, France; Energy Transducing Systems and Mitochondrial Morphology, Université de Bordeaux, Bordeaux, France
| | - Diego González-Halphen
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México, Mexico.
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104
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Human cytomegalovirus US21 protein is a viroporin that modulates calcium homeostasis and protects cells against apoptosis. Proc Natl Acad Sci U S A 2018; 115:E12370-E12377. [PMID: 30530673 DOI: 10.1073/pnas.1813183115] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The human cytomegalovirus (HCMV) US12 gene family comprises a set of 10 contiguous genes (US12 to US21) with emerging roles in the regulation of virus cell tropism, virion composition, and immunoevasion. Of all of the US12 gene products, pUS21 shows the highest level of identity with two cellular transmembrane BAX inhibitor motif-containing (TMBIM) proteins: Bax inhibitor-1 and Golgi anti-apoptotic protein, both of which are involved in the regulation of cellular Ca2+ homeostasis and adaptive cell responses to stress conditions. Here, we report the US21 protein to be a viral-encoded ion channel that regulates intracellular Ca2+ homeostasis and protects cells against apoptosis. Indeed, we show pUS21 to be a 7TMD protein expressed with late kinetics that accumulates in ER-derived vesicles. Deletion or inactivation of the US21 gene resulted in reduced HCMV growth, even in fibroblasts, due to reduced gene expression. Ratiometric fluorescence imaging assays revealed that expression of pUS21 reduces the Ca2+ content of intracellular ER stores. An increase in cell resistance to intrinsic apoptosis was then observed as an important cytobiological consequence of the pUS21-mediated alteration of intracellular Ca2+ homeostasis. Moreover, a single point mutation in the putative pore of pUS21 impaired the reduction of ER Ca2+ concentration and attenuated the antiapoptotic activity of pUS21wt, supporting a functional link with its ability to manipulate Ca2+ homeostasis. Together, these results suggest pUS21 of HCMV constitutes a TMBIM-derived viroporin that may contribute to HCMV's overall strategy to counteract apoptosis in infected cells.
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105
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Reuter G, Pankovics P, Boros Á. Nonsuppurative (Aseptic) Meningoencephalomyelitis Associated with Neurovirulent Astrovirus Infections in Humans and Animals. Clin Microbiol Rev 2018; 31:e00040-18. [PMID: 30158300 PMCID: PMC6148189 DOI: 10.1128/cmr.00040-18] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Astroviruses are thought to be enteric pathogens. Since 2010, a certain group of astroviruses has increasingly been recognized, using up-to-date random amplification and high-throughput next-generation sequencing (NGS) methods, as potential neurovirulent (Ni) pathogens of severe central nervous system (CNS) infections, causing encephalitis, meningoencephalitis, and meningoencephalomyelitis. To date, neurovirulent astrovirus cases or epidemics have been reported for humans and domesticated mammals, including mink, bovines, ovines, and swine. This comprehensive review summarizes the virology, epidemiology, pathology, diagnosis, therapy, and future perspective related to neurovirulent astroviruses in humans and mammals, based on a total of 30 relevant articles available in PubMed (searched by use of the terms "astrovirus/encephalitis" and "astrovirus/meningitis" on 2 March 2018). A paradigm shift should be considered based on the increasing knowledge of the causality-effect association between neurotropic astroviruses and CNS infection, and attention should be drawn to the role of astroviruses in unknown CNS diseases.
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Affiliation(s)
- Gábor Reuter
- Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
| | - Péter Pankovics
- Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
| | - Ákos Boros
- Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
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106
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Shey RA, Ghogomu SM, Njume FN, Gainkam LOT, Poelvoorde P, Mutesa L, Robert A, Humblet P, Munyampundu JP, Kamgno J, Lelubre C, Vanhamme L, Souopgui J. Prediction and validation of the structural features of Ov58GPCR, an immunogenic determinant of Onchocerca volvulus. PLoS One 2018; 13:e0202915. [PMID: 30256790 PMCID: PMC6157839 DOI: 10.1371/journal.pone.0202915] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 08/11/2018] [Indexed: 11/18/2022] Open
Abstract
Onchocerciasis is a severely debilitating yet neglected tropical disease (NTD) that creates social stigma, generates and perpetuates poverty, and leads ultimately in some cases to irreversible unilateral or bilateral blindness if untreated. Consequently, the disease is a major impediment to socioeconomic development. Many control programs have been launched for the disease with moderate successes achieved. This mitigated hit is partially due to the lingering need for reliable, non-invasive and easily applicable tools for mapping endemic regions and post-elimination surveillance. In this work, bioinformatics analyses combined with immunological assays were applied in a bid to develop potential tools for diagnosis and assessing the success of drug treatment programs. We report that (i) the O. volvulus antigen, Ov58GPCR is a G-protein coupled receptor (GPCR) conserved in related nematodes, (ii) synthetic peptides predicted to be in the extracellular domain (ECD) of Ov58GPCR are indeed immunogenic epitopes in actively-infected individuals, (iii) synthetic peptide cocktails discriminate between actively-infected individuals, treated individuals and healthy African controls, (iv) polyclonal antibodies against one of the peptides or against the bacterially-expressed ECD reacted specifically with the native antigen of O. volvulus total and surface extracts, (v) Ov58GPCR is transcribed in both larvae and adult parasite stages, (vi) IgG and IgE responses to the recombinant ECD decline with ivermectin treatment. All these findings suggest that the extracellular domain and synthetic peptides of Ov58GPCR, as well as the specific immune response generated could be harnessed in the context of disease diagnosis and surveillance.
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Affiliation(s)
- Robert Adamu Shey
- Department of Molecular Biology, Institute of Biology and Molecular Medicine, IBMM Universite Libre de Bruxelles, Gosselies Campus, Gosselies, Hainaut, Belgium
- Molecular and Cell Biology Laboratory, Biotechnology Unit, Faculty of Science, University of Buea, Buea, Cameroon
| | - Stephen Mbigha Ghogomu
- Molecular and Cell Biology Laboratory, Biotechnology Unit, Faculty of Science, University of Buea, Buea, Cameroon
| | - Ferdinand Ngale Njume
- Department of Molecular Biology, Institute of Biology and Molecular Medicine, IBMM Universite Libre de Bruxelles, Gosselies Campus, Gosselies, Hainaut, Belgium
- Molecular and Cell Biology Laboratory, Biotechnology Unit, Faculty of Science, University of Buea, Buea, Cameroon
| | - Lea Olive Tchouate Gainkam
- Department of Molecular Biology, Institute of Biology and Molecular Medicine, IBMM Universite Libre de Bruxelles, Gosselies Campus, Gosselies, Hainaut, Belgium
| | - Philippe Poelvoorde
- Department of Molecular Biology, Institute of Biology and Molecular Medicine, IBMM Universite Libre de Bruxelles, Gosselies Campus, Gosselies, Hainaut, Belgium
| | - Leon Mutesa
- Center for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | - Annie Robert
- Faculté de santé publique, Institut de recherche expérimentale et clinique, Pôle d'épidémiologie et biostatistique, Université Catholique de Louvain, Clos Chapelle-aux-champs, Woluwe-Saint-Lambert, Belgium
| | - Perrine Humblet
- École de santé publique, Université Libre de Bruxelles, Bruxelles, Belgium
| | - Jean-Pierre Munyampundu
- Center for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | - Joseph Kamgno
- Department of Epidemiology, Centre for research on filariasis and other tropical diseases, (CRFilMT), Yaoundé, Cameroon
| | - Christophe Lelubre
- Laboratoire de Médecine Expérimentale, Université Libre de Bruxelles (ULB) - Unité 222, CHU Charleroi (Hôpital André Vésale), Montigny-Le-Tilleul, Belgium
| | - Luc Vanhamme
- Department of Molecular Biology, Institute of Biology and Molecular Medicine, IBMM Universite Libre de Bruxelles, Gosselies Campus, Gosselies, Hainaut, Belgium
| | - Jacob Souopgui
- Department of Molecular Biology, Institute of Biology and Molecular Medicine, IBMM Universite Libre de Bruxelles, Gosselies Campus, Gosselies, Hainaut, Belgium
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107
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Naureen Z, Sham A, Al Ashram H, Gilani SA, Al Gheilani S, Mabood F, Hussain J, Al Harrasi A, AbuQamar SF. Effect of phosphate nutrition on growth, physiology and phosphate transporter expression of cucumber seedlings. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 127:211-222. [PMID: 29614440 DOI: 10.1016/j.plaphy.2018.03.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 03/22/2018] [Accepted: 03/23/2018] [Indexed: 06/08/2023]
Abstract
Although abundantly present in soils, inorganic phosphate (Pi) acquisition by plants is highly dependent on the transmembrane phosphate transporter (PT) gene family. Cucumber (Cucumis sativus) requires a large amount of phosphorus (P). The purpose of this study was to isolate the CsPT2-1 from cucumber roots, and to determine the influence of Pi nutrition on cucumber growth, metabolism and transcript levels of CsPT2-1 in tissues. Full length CsPT2-1 was cloned and phylogenetically identified. In two greenhouse experiments, P-deficient seedlings provided with low or high P concentrations were sampled at 10 and 21 days post treatment, respectively. Addition of P dramatically reduced growth of roots but not shoots. Supplying plants with high P resulted in increased total protein in leaves. Acid phosphatase activity increased significantly in leaves at any rate higher than 4 mM P. Increasing P concentration had a notable decrease in glucose concentrations in leaves of plants supplied with >0.5 mM P. In roots, glucose and starch concentrations increased with increasing P supply. Steady-state transcript levels of CsPT2-1 were high in P-deprived roots, but declined when plants were provided >10 mM P. To our knowledge, this is the first report focusing on a PT and its expression levels in cucumber.
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Affiliation(s)
- Zakira Naureen
- Department of Biological Sciences and Chemistry, University of Nizwa, Nizwa, Oman
| | - Arjun Sham
- Department of Biology, United Arab Emirates University, P.O. Box 15551, Al-Ain, United Arab Emirates
| | - Hibatullah Al Ashram
- Department of Biology, United Arab Emirates University, P.O. Box 15551, Al-Ain, United Arab Emirates
| | - Syed A Gilani
- Department of Biological Sciences and Chemistry, University of Nizwa, Nizwa, Oman
| | - Salma Al Gheilani
- Department of Biological Sciences and Chemistry, University of Nizwa, Nizwa, Oman
| | - Fazal Mabood
- Department of Biological Sciences and Chemistry, University of Nizwa, Nizwa, Oman
| | - Javid Hussain
- Department of Biological Sciences and Chemistry, University of Nizwa, Nizwa, Oman
| | - Ahmed Al Harrasi
- UoN Chair of Oman's Medicinal Plants and Marine Natural Products, University of Nizwa, Oman
| | - Synan F AbuQamar
- Department of Biology, United Arab Emirates University, P.O. Box 15551, Al-Ain, United Arab Emirates.
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108
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Kundu S, Sharma R. Origin, evolution, and divergence of plant class C GH9 endoglucanases. BMC Evol Biol 2018; 18:79. [PMID: 29848310 PMCID: PMC5977491 DOI: 10.1186/s12862-018-1185-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 04/18/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Glycoside hydrolases of the GH9 family encode cellulases that predominantly function as endoglucanases and have wide applications in the food, paper, pharmaceutical, and biofuel industries. The partitioning of plant GH9 endoglucanases, into classes A, B, and C, is based on the differential presence of transmembrane, signal peptide, and the carbohydrate binding module (CBM49). There is considerable debate on the distribution and the functions of these enzymes which may vary in different organisms. In light of these findings we examined the origin, emergence, and subsequent divergence of plant GH9 endoglucanases, with an emphasis on elucidating the role of CBM49 in the digestion of crystalline cellulose by class C members. RESULTS Since, the digestion of crystalline cellulose mandates the presence of a well-defined set of aromatic and polar amino acids and/or an attributable domain that can mediate this conversion, we hypothesize a vertical mode of transfer of genes that could favour the emergence of class C like GH9 endoglucanase activity in land plants from potentially ancestral non plant taxa. We demonstrated the concomitant occurrence of a GH9 domain with CBM49 and other homologous carbohydrate binding modules, in putative endoglucanase sequences from several non-plant taxa. In the absence of comparable full length CBMs, we have characterized several low strength patterns that could approximate the CBM49, thereby, extending support for digestion of crystalline cellulose to other segments of the protein. We also provide data suggestive of the ancestral role of putative class C GH9 endoglucanases in land plants, which includes detailed phylogenetics and the presence and subsequent loss of CBM49, transmembrane, and signal peptide regions in certain populations of early land plants. These findings suggest that classes A and B of modern vascular land plants may have emerged by diverging directly from CBM49 encompassing putative class C enzymes. CONCLUSION Our detailed phylogenetic and bioinformatics analysis of putative GH9 endoglucanase sequences across major taxa suggests that plant class C enzymes, despite their recent discovery, could function as the last common ancestor of classes A and B. Additionally, research into their ability to digest or inter-convert crystalline and amorphous forms of cellulose could make them lucrative candidates for engineering biofuel feedstock.
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Affiliation(s)
- Siddhartha Kundu
- Department of Biochemistry, Government of NCT of Delhi, Dr. Baba Saheb Ambedkar Medical College & Hospital, New Delhi, 110085, India. .,Crop Genetics and Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Rita Sharma
- Crop Genetics and Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
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109
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Wilson LD, Obakpolor OA, Jones AM, Richie AL, Mieczkowski BD, Fall GT, Hall RW, Rumbley JN, Kroft TL. The Caenorhabditis elegans spe-49 gene is required for fertilization and encodes a sperm-specific transmembrane protein homologous to SPE-42. Mol Reprod Dev 2018; 85:563-578. [PMID: 29693775 DOI: 10.1002/mrd.22992] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 04/20/2018] [Indexed: 01/13/2023]
Abstract
Fertilization, the fusion of sperm and oocyte to form a zygote, is the first and arguably the most important cell-cell interaction event in an organism's life. Forward and reverse genetic approaches in the nematode Caenorhabditis elegans have identified many genes that are required for gametogenesis and fertilization and thus are beginning to elucidate the molecular pathways that underlie these processes. We identified an allele of the spe-49 gene in a second filial generation (F2 ) mutagenesis screen for spermatogenesis-defective (spe) mutants. Mutant worms for spe-49 produce sperm that have normal morphology, activate to form ameboid spermatozoa, and can migrate to and maintain their position in the hermaphrodite reproductive tract but fail to fertilize oocytes. This phenotype puts spe-49 in the spe-9 class of late-acting genes that function in sperm at the time of fertilization. We cloned the spe-49 gene through a combination of deficiency mapping, transgenic rescue, and genomic sequencing. spe-49 messenger RNA (mRNA) is enriched in male germ cells, and the complementary DNA (cDNA) encodes a predicted 772-amino-acid six-pass transmembrane protein that is homologous to SPE-42. Indeed, SPE-49 and SPE-42 have identical predicted membrane topology and domain structure, including a large extracellular domain with six conserved cysteine residues, a DC-STAMP domain, and a C-terminal cytoplasmic domain containing a C4-C4 RING finger motif. The presence of two SPE-42 homologs in animal genomes from worms to humans suggests that these proteins are highly conserved components of the molecular apparatus required for the sperm-oocyte recognition, binding, and fusion.
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Affiliation(s)
- Luke D Wilson
- Department of Anatomic Pathology, Mayo Clinic, Rochester, Minnesota
| | - Omoyemwen A Obakpolor
- Department of Biology, College of Sciences, Auburn University at Montgomery, Montgomery, Alabama
| | - Autumn M Jones
- Department of Biology, College of Sciences, Auburn University at Montgomery, Montgomery, Alabama
| | | | | | - Gabriel T Fall
- Reagent Quality Control, Division of Diagnostics, Beckman Coulter, Chaska, Minnesota
| | - Rosine W Hall
- Department of Biology, College of Sciences, Auburn University at Montgomery, Montgomery, Alabama
| | - Jon N Rumbley
- Department of Pharmacy Practice and Pharmaceutical Sciences, College of Pharmacy, University of Minnesota Duluth, Duluth, Minnesota
| | - Tim L Kroft
- Department of Biology, College of Sciences, Auburn University at Montgomery, Montgomery, Alabama
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110
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Wang H, Wang J, Zhang L, Sun P, Du N, Li Y. A Sequential Segment Based Alpha-Helical Transmembrane Protein Alignment Method. Int J Biol Sci 2018; 14:901-906. [PMID: 29989071 PMCID: PMC6036746 DOI: 10.7150/ijbs.24327] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 02/02/2018] [Indexed: 11/29/2022] Open
Abstract
Alpha-helical transmembrane protein (αTMP) is one of the two major categories of transmembrane protein (TMP). They are abundant existing in eukaryotic cells and involved in many biological processes. The special physicochemical properties, the structures of αTMP are hard to be experimentally solved, but αTMP's sequential segments are important to determine their conformations, so that TM-specific alignment is necessary to benefit their structure prediction. We used segment information extracted from topology structure and evolutionary information as features to implement a αTMP Segment Alignment method (TMSA). The method was trained using one non-redundant dataset and tested using another non-redundant dataset. Comparing the results to a general alignment method HHalign, TMSA achieved higher alignment accuracy, and easier to recognize the fold of αTMPs.
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Affiliation(s)
- Han Wang
- School of Information Science and Technology, Northeast Normal University, Changchun, 130117, China.,Institute of Computational Biology, Northeast Normal University, Changchun, 130117, China
| | - Jingru Wang
- School of Information Science and Technology, Northeast Normal University, Changchun, 130117, China.,Institute of Computational Biology, Northeast Normal University, Changchun, 130117, China
| | - Li Zhang
- School of Computer Science and Engineering, Changchun University of Technology, Changchun, China
| | - Pingping Sun
- School of Information Science and Technology, Northeast Normal University, Changchun, 130117, China.,Institute of Computational Biology, Northeast Normal University, Changchun, 130117, China
| | - Ning Du
- School of Mathematics and Statistics, Northeast Normal University, Changchun, 130024, China
| | - Yanwen Li
- School of Information Science and Technology, Northeast Normal University, Changchun, 130117, China.,Institute of Computational Biology, Northeast Normal University, Changchun, 130117, China
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111
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Chan CYL, Hiong KC, Boo MV, Choo CYL, Wong WP, Chew SF, Ip YK. Light exposure enhances urea absorption in the fluted giant clam, Tridacna squamosa, and up-regulates the protein abundance of a light-dependent urea active transporter, DUR3-like, in its ctenidium. J Exp Biol 2018; 221:jeb176313. [PMID: 29540461 DOI: 10.1242/jeb.176313] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 03/12/2018] [Indexed: 12/26/2022]
Abstract
Giant clams live in nutrient-poor reef waters of the Indo-Pacific and rely on symbiotic dinoflagellates (Symbiodinium spp., also known as zooxanthellae) for nutrients. As the symbionts are nitrogen deficient, the host clam has to absorb exogenous nitrogen and supply it to them. This study aimed to demonstrate light-enhanced urea absorption in the fluted giant clam, Tridacna squamosa, and to clone and characterize the urea active transporter DUR3-like from its ctenidium (gill). The results indicate that T. squamosa absorbs exogenous urea, and the rate of urea uptake in the light was significantly higher than that in darkness. The DUR3-like coding sequence obtained from its ctenidium comprised 2346 bp, encoding a protein of 782 amino acids and 87.0 kDa. DUR3-like was expressed strongly in the ctenidium, outer mantle and kidney. Twelve hours of exposure to light had no significant effect on the transcript level of ctenidial DUR3-like However, between 3 and 12 h of light exposure, DUR3-like protein abundance increased progressively in the ctenidium, and became significantly greater than that in the control at 12 h. DUR3-like had an apical localization in the epithelia of the ctenidial filaments and tertiary water channels. Taken together, these results indicate that DUR3-like might participate in light-enhanced urea absorption in the ctenidium of T. squamosa When made available to the symbiotic zooxanthellae that are known to possess urease, the absorbed urea can be metabolized to NH3 and CO2 to support amino acid synthesis and photosynthesis, respectively, during insolation.
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Affiliation(s)
- Christabel Y L Chan
- Department of Biological Sciences, National University of Singapore, Kent Ridge, Singapore 117543, Republic of Singapore
| | - Kum C Hiong
- Department of Biological Sciences, National University of Singapore, Kent Ridge, Singapore 117543, Republic of Singapore
| | - Mel V Boo
- Department of Biological Sciences, National University of Singapore, Kent Ridge, Singapore 117543, Republic of Singapore
| | - Celine Y L Choo
- Department of Biological Sciences, National University of Singapore, Kent Ridge, Singapore 117543, Republic of Singapore
| | - Wai P Wong
- Department of Biological Sciences, National University of Singapore, Kent Ridge, Singapore 117543, Republic of Singapore
| | - Shit F Chew
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, 1 Nanyang Walk, Singapore 637616, Republic of Singapore
| | - Yuen K Ip
- Department of Biological Sciences, National University of Singapore, Kent Ridge, Singapore 117543, Republic of Singapore
- The Tropical Marine Science Institute, National University of Singapore, Kent Ridge, Singapore 119227, Republic of Singapore
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112
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Tidhar R, Zelnik ID, Volpert G, Ben-Dor S, Kelly S, Merrill AH, Futerman AH. Eleven residues determine the acyl chain specificity of ceramide synthases. J Biol Chem 2018; 293:9912-9921. [PMID: 29632068 DOI: 10.1074/jbc.ra118.001936] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 03/19/2018] [Indexed: 01/08/2023] Open
Abstract
Lipids display large structural complexity, with ∼40,000 different lipids identified to date, ∼4000 of which are sphingolipids. A critical factor determining the biological activities of the sphingolipid, ceramide, and of more complex sphingolipids is their N-acyl chain length, which in mammals is determined by a family of six ceramide synthases (CerS). Little information is available about the CerS regions that determine specificity toward different acyl-CoA substrates. We previously demonstrated that substrate specificity resides in a region of ∼150 residues in the Tram-Lag-CLN8 domain. Using site-directed mutagenesis and biochemical analyses, we now narrow specificity down to an 11-residue sequence in a loop located between the last two putative transmembrane domains (TMDs) of the CerS. The specificity of a chimeric protein, CerS5(299-309→CerS2), based on the backbone of CerS5 (which generates C16-ceramide), but containing 11 residues from CerS2 (which generates C22-C24-ceramides), was altered such that it generated C22-C24 and other ceramides. Moreover, a chimeric protein, CerS4(291-301→CerS2), based on CerS4 (which normally generates C18-C22 ceramides) displayed significant activity toward C24:1-CoA. Additional data supported the notion that substitutions of these 11 residues alter the specificities of the CerS toward their cognate acyl-CoAs. Our findings may suggest that this short loop may restrict adjacent TMDs, leading to a more open conformation in the membrane, and that the CerS acting on shorter acyl-CoAs may have a longer, more flexible loop, permitting TMD flexibility. In summary, we have identified an 11-residue region that determines the acyl-CoA specificity of CerS.
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Affiliation(s)
- Rotem Tidhar
- From the Department of Biomolecular Sciences and
| | | | | | - Shifra Ben-Dor
- the Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 76100, Israel and
| | - Samuel Kelly
- the School of Biology and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332-0230
| | - Alfred H Merrill
- the School of Biology and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332-0230
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113
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Niitsu A, Heal JW, Fauland K, Thomson AR, Woolfson DN. Membrane-spanning α-helical barrels as tractable protein-design targets. Philos Trans R Soc Lond B Biol Sci 2018. [PMID: 28630153 DOI: 10.1098/rstb.2016.0213] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The rational (de novo) design of membrane-spanning proteins lags behind that for water-soluble globular proteins. This is due to gaps in our knowledge of membrane-protein structure, and experimental difficulties in studying such proteins compared to water-soluble counterparts. One limiting factor is the small number of experimentally determined three-dimensional structures for transmembrane proteins. By contrast, many tens of thousands of globular protein structures provide a rich source of 'scaffolds' for protein design, and the means to garner sequence-to-structure relationships to guide the design process. The α-helical coiled coil is a protein-structure element found in both globular and membrane proteins, where it cements a variety of helix-helix interactions and helical bundles. Our deep understanding of coiled coils has enabled a large number of successful de novo designs. For one class, the α-helical barrels-that is, symmetric bundles of five or more helices with central accessible channels-there are both water-soluble and membrane-spanning examples. Recent computational designs of water-soluble α-helical barrels with five to seven helices have advanced the design field considerably. Here we identify and classify analogous and more complicated membrane-spanning α-helical barrels from the Protein Data Bank. These provide tantalizing but tractable targets for protein engineering and de novo protein design.This article is part of the themed issue 'Membrane pores: from structure and assembly, to medicine and technology'.
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Affiliation(s)
- Ai Niitsu
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Jack W Heal
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Kerstin Fauland
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Andrew R Thomson
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Derek N Woolfson
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK .,School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, UK.,BrisSynBio, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
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114
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Abstract
Many computational methods are available for predicting protein sorting in bacteria. When comparing them, it is important to know that they can be grouped into three fundamentally different approaches: signal-based, global-property-based and homology-based prediction. In this chapter, the strengths and drawbacks of each of these approaches is described through many examples of methods that predict secretion, integration into membranes, or subcellular locations in general. The aim of this chapter is to provide a user-level introduction to the field with a minimum of computational theory.
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Affiliation(s)
- Henrik Nielsen
- Technical University of Denmark, Kemitorvet, Building 208, DK-2800, Kgs. Lyngby, Denmark.
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115
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Abstract
As a protective envelope surrounding the bacterial cell, the peptidoglycan sacculus is a site of vulnerability and an antibiotic target. Peptidoglycan components, assembled in the cytoplasm, are shuttled across the membrane in a cycle that uses undecaprenyl-phosphate. A product of peptidoglycan synthesis, undecaprenyl-pyrophosphate, is converted to undecaprenyl-phosphate for reuse in the cycle by the membrane integral pyrophosphatase, BacA. To understand how BacA functions, we determine its crystal structure at 2.6 Å resolution. The enzyme is open to the periplasm and to the periplasmic leaflet via a pocket that extends into the membrane. Conserved residues map to the pocket where pyrophosphorolysis occurs. BacA incorporates an interdigitated inverted topology repeat, a topology type thus far only reported in transporters and channels. This unique topology raises issues regarding the ancestry of BacA, the possibility that BacA has alternate active sites on either side of the membrane and its possible function as a flippase. Bacterial cell wall components are assembled in a transmembrane cycle that involves the membrane integral pyrophosphorylase, BacA. Here the authors solve the crystal structure of BacA which shows an interdigitated inverted topology repeat that hints towards a flippase function for BacA.
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116
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Jeřábek P, Florián J, Martínek V. Lipid molecules can induce an opening of membrane-facing tunnels in cytochrome P450 1A2. Phys Chem Chem Phys 2018; 18:30344-30356. [PMID: 27722524 DOI: 10.1039/c6cp03692a] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cytochrome P450 1A2 (P450 1A2, CYP1A2) is a membrane-bound enzyme that oxidizes a broad range of hydrophobic substrates. The structure and dynamics of both the catalytic and trans-membrane (TM) domains of this enzyme in the membrane/water environment were investigated using a multiscale computational approach, including coarse-grained and all-atom molecular dynamics. Starting from the spontaneous self-assembly of the system containing the TM or soluble domain immersed in randomized dilauroyl phosphatidylcholine (DLPC)/water mixture into their respective membrane-bound forms, we reconstituted the membrane-bound structure of the full-length P450 1A2. This structure includes a TM helix that spans the membrane, while being connected to the catalytic domain by a short flexible loop. Furthermore, in this model, the upper part of the TM helix interacts directly with a conserved and highly hydrophobic N-terminal proline-rich segment of the catalytic domain; this segment and the FG loop are immersed in the membrane, whereas the remaining portion of the catalytic domain remains exposed to aqueous solution. The shallow membrane immersion of the catalytic domain induces a depression in the opposite intact layer of the phospholipids. This structural effect may help in stabilizing the position of the TM helix directly beneath the catalytic domain. The partial immersion of the catalytic domain also allows for the enzyme substrates to enter the active site from either aqueous solution or phospholipid environment via several solvent- and membrane-facing tunnels in the full-length P450 1A2. The calculated tunnel dynamics indicated that the opening probability of the membrane-facing tunnels is significantly enhanced when a DLPC molecule spontaneously penetrates into the membrane-facing tunnel 2d. The energetics of the lipid penetration process were assessed by the linear interaction energy (LIE) approximation, and found to be thermodynamically feasible.
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Affiliation(s)
- Petr Jeřábek
- Department of Biochemistry, Charles University, Faculty of Science, Albertov 2030, 128 43 Prague 2, Czech Republic
| | - Jan Florián
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 W. Sheridan Rd., Chicago, IL 60660, USA
| | - Václav Martínek
- Department of Biochemistry, Charles University, Faculty of Science, Albertov 2030, 128 43 Prague 2, Czech Republic and Department of Teaching and Didactics of Chemistry, Charles University, Faculty of Science, Albertov 3, 128 43 Prague 2, Czech Republic.
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117
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Li B, Fooksa M, Heinze S, Meiler J. Finding the needle in the haystack: towards solving the protein-folding problem computationally. Crit Rev Biochem Mol Biol 2018; 53:1-28. [PMID: 28976219 PMCID: PMC6790072 DOI: 10.1080/10409238.2017.1380596] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 08/22/2017] [Accepted: 09/13/2017] [Indexed: 12/22/2022]
Abstract
Prediction of protein tertiary structures from amino acid sequence and understanding the mechanisms of how proteins fold, collectively known as "the protein folding problem," has been a grand challenge in molecular biology for over half a century. Theories have been developed that provide us with an unprecedented understanding of protein folding mechanisms. However, computational simulation of protein folding is still difficult, and prediction of protein tertiary structure from amino acid sequence is an unsolved problem. Progress toward a satisfying solution has been slow due to challenges in sampling the vast conformational space and deriving sufficiently accurate energy functions. Nevertheless, several techniques and algorithms have been adopted to overcome these challenges, and the last two decades have seen exciting advances in enhanced sampling algorithms, computational power and tertiary structure prediction methodologies. This review aims at summarizing these computational techniques, specifically conformational sampling algorithms and energy approximations that have been frequently used to study protein-folding mechanisms or to de novo predict protein tertiary structures. We hope that this review can serve as an overview on how the protein-folding problem can be studied computationally and, in cases where experimental approaches are prohibitive, help the researcher choose the most relevant computational approach for the problem at hand. We conclude with a summary of current challenges faced and an outlook on potential future directions.
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Affiliation(s)
- Bian Li
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Michaela Fooksa
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
- Chemical and Physical Biology Graduate Program, Vanderbilt University, Nashville, TN, USA
| | - Sten Heinze
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
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118
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Predicting Alpha Helical Transmembrane Proteins Using HMMs. Methods Mol Biol 2018; 1552:63-82. [PMID: 28224491 DOI: 10.1007/978-1-4939-6753-7_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Alpha helical transmembrane (TM) proteins constitute an important structural class of membrane proteins involved in a wide variety of cellular functions. The prediction of their transmembrane topology, as well as their discrimination in newly sequenced genomes, is of great importance for the elucidation of their structure and function. Several methods have been applied for the prediction of the transmembrane segments and the topology of alpha helical transmembrane proteins utilizing different algorithmic techniques. Hidden Markov Models (HMMs) have been efficiently used in the development of several computational methods used for this task. In this chapter we give a brief review of different available prediction methods for alpha helical transmembrane proteins pointing out sequence and structural features that should be incorporated in a prediction method. We then describe the procedure of the design and development of a Hidden Markov Model capable of predicting the transmembrane alpha helices in proteins and discriminating them from globular proteins.
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119
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Rani S, Pooja K. Elucidation of structural and functional characteristics of collagenase from Pseudomonas aeruginosa. Process Biochem 2018. [DOI: 10.1016/j.procbio.2017.09.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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120
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Pandey V, Krishnan V, Basak N, Marathe A, Thimmegowda V, Dahuja A, Jolly M, Sachdev A. Molecular modeling and in silico characterization of GmABCC5: a phytate transporter and potential target for low-phytate crops. 3 Biotech 2018; 8:54. [PMID: 29354365 DOI: 10.1007/s13205-017-1053-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 12/17/2017] [Indexed: 02/06/2023] Open
Abstract
Designing low-phytate crops without affecting the developmental process in plants had led to the identification of ABCC5 gene in soybean. The GmABCC5 gene was identified and a partial gene sequence was cloned from popular Indian soybean genotype Pusa16. Conserved domains and motifs unique to ABC transporters were identified in the 30 homologous sequences retrieved by BLASTP analysis. The homologs were analyzed for their evolutionary relationship and physiochemical properties. Conserved domains, transmembrane architecture and secondary structure of GmABCC5 were predicted with the aid of computational tools. Analysis identified 53 alpha helices and 31 beta strands, predicting 60% residues in alpha conformation. A three-dimensional (3D) model for GmABCC5 was developed based on 5twv.1.B (Homo sapiens) template homology to gain better insight into its molecular mechanism of transport and sequestration. Spatio-temporal real-time PCR analysis identified mid-to-late seed developmental stages as the time window for the maximum GmABCC5 gene expression, a potential target stage for phytate reduction. Results of this study provide valuable insights into the structural and functional characteristics of GmABCC5, which may be further utilized for the development of nutritionally enriched low-phytate soybean with improved mineral bioavailability.
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Affiliation(s)
- Vanita Pandey
- 1Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
- Quality and Basic Sciences, ICAR-Indian Institute of Wheat and Barley Research, Karnal, New Delhi 132 001 India
| | - Veda Krishnan
- 1Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Nabaneeta Basak
- 1Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
- Crop Physiology and Biochemistry, ICAR-National Rice Research Institute, Cuttack, 753006 India
| | - Ashish Marathe
- 1Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Vinutha Thimmegowda
- 1Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Anil Dahuja
- 1Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Monica Jolly
- 1Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Archana Sachdev
- 1Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
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121
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Jeiranikhameneh M, Razavi MR, Irani S, Siadat SD, Oloomi M. Designing novel construction for cell surface display of protein E on Escherichia coli using non-classical pathway based on Lpp-OmpA. AMB Express 2017; 7:53. [PMID: 28247289 PMCID: PMC5331024 DOI: 10.1186/s13568-017-0350-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 02/20/2017] [Indexed: 01/30/2023] Open
Abstract
Today, transference of recombinant protein on the outer surface of bacteria is deemed as a valuable process for various applications in biotechnology including preparation of vaccines. In this study, Lpp-OmpA structure was used to present outer membrane protein E of Haemophilus influenzae on E. coli outer membrane. Also, a structure was designed according to Lpp-OmpA based on non-classical secretion pathway using bioinformatics software such as MEMSAT-SVM, ScrotumP and SignalP where it lacked any signal peptide at its N-terminal. Potential of this structure in the presentation of protein E on the surface of E. coli through non-classical pathway was indicated by western blotting, SDS page and fluorescent microscopy techniques, similarly its effectiveness was compared with Lpp-OmpA system. The results of the current study showed that the new structure had higher efficiency than Lpp-OmpA, and it could transport protein E on outer membrane well. This study is the first report in the presentation of H. influenzae PE onto the surface of E. coli by Lpp-OmpA, and the structure originated from Lpp-OmpA, according to the non-classical secretion pathway. Our results suggest that non-classical secretion pathway may be exploited as a new secretory pathway on the outer surface of the cell for recombinant proteins.
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122
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Jackson GE, Pavadai E, Gäde G, Timol Z, Andersen NH. Data for the homology modelling of the red pigment-concentrating hormone receptor (Dappu-RPCHR) of the crustacean Daphnia pulex, and docking of its cognate agonist (Dappu-RPCH). Data Brief 2017; 15:941-947. [PMID: 29159233 PMCID: PMC5683752 DOI: 10.1016/j.dib.2017.10.045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 10/13/2017] [Accepted: 10/19/2017] [Indexed: 11/23/2022] Open
Abstract
The data presented in this article are related to the publication “Interaction of the red pigment-concentrating hormone of the crustacean Daphnia pulex, with its cognate receptor, Dappu-RPCHR: A nuclear magnetic resonance and modeling study” (Jackson et al., 2017) [1]. This article contains the data for homology modeling of the red pigment-concentrating hormone (RPCH) receptor of the water flea, Daphnia pulex (Dappu-RPCHR), which was constructed from its primary sequence. This is the first 3D model of a crustacean G-protein coupled receptor. Docking of the agonist, pGlu-Val-Asn-Phe-Ser-Thr-Ser-Trp amide (Dappu-RPCH), was used to find a binding pocket on the receptor and compared to the binding pocket of the adipokinetic hormone (AKH) receptor from the malaria mosquito. Data for the receptor, with and without loop refinement, together with the docked agonist, are presented.
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Affiliation(s)
- Graham E Jackson
- Department of Chemistry, University of Cape Town, Private Bag, Rondebosch, Cape Town 7701, South Africa
| | - Elumalai Pavadai
- Department of Chemistry, University of Cape Town, Private Bag, Rondebosch, Cape Town 7701, South Africa
| | - Gerd Gäde
- Biological Sciences, University of Cape Town, Private Bag, Rondebosch, Cape Town 7701, South Africa
| | - Zaheer Timol
- Department of Chemistry, University of Cape Town, Private Bag, Rondebosch, Cape Town 7701, South Africa
| | - Niels H Andersen
- Chemistry Department, University of Washington, Seattle, WA 98195, United States
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123
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Dynamic regulation of CD28 conformation and signaling by charged lipids and ions. Nat Struct Mol Biol 2017; 24:1081-1092. [PMID: 29058713 DOI: 10.1038/nsmb.3489] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 09/21/2017] [Indexed: 12/21/2022]
Abstract
CD28 provides an essential costimulatory signal for T cell activation, and its function is critical in antitumor immunity. However, the molecular mechanism of CD28 transmembrane signaling remains elusive. Here we show that the conformation and signaling of CD28 are regulated by two counteractive charged factors, acidic phospholipids and Ca2+ ions. NMR spectroscopy analyses showed that acidic phospholipids can sequester CD28 signaling motifs within the membrane, thereby limiting CD28 basal signaling. T cell receptor (TCR) activation induced an increase in the local Ca2+ concentration around CD28, and Ca2+ directly disrupted CD28-lipid interaction, leading to opening and signaling of CD28. We observed that the TCR, Ca2+, and CD28 together form a dual-positive-feedback circuit that substantially amplifies T cell signaling and thus increases antigen sensitivity. This work unravels a new regulatory mechanism for CD28 signaling and thus contributes to the understanding of the dependence of costimulation signaling on TCR signaling and the high sensitivity of T cells.
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124
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Parthasarathy S, Parapatla H, Siddavattam D. Topological analysis of the lipoprotein organophosphate hydrolase from Sphingopyxis wildii reveals a periplasmic localisation. FEMS Microbiol Lett 2017; 364:4101234. [PMID: 28957456 DOI: 10.1093/femsle/fnx187] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 08/30/2017] [Indexed: 11/14/2022] Open
Abstract
Organophosphate hydrolase (OPH) is a membrane-associated lipoprotein. It translocates across the inner membrane via the twin-arginine transport pathway and remains anchored to the periplasmic face of the inner membrane through a diacylglycerol moiety linked to the invariant cysteine residue found at the junction of a SpaseII cleavage site. Due to the existence of a transmembrane helix at the C-terminus of the mature OPH, an inner-membrane topology was predicted suggesting the C-terminus of OPH is cytoplasmic. The predicted topology was validated by generating OPH variants either fused in-frame with β-lactamase or with unique cysteine residues. Sphingopyxis wildii cells expressing OPH variants with Bla fused at the N-terminal, C-terminal or central regions all grew in the presence of ampicillin. Supporting the β-lactamase reporter assay, the OPH variants having unique cysteine residues at different strategic locations were accessible to the otherwise membrane-impermeant PEG-Mal (methoxypolyethylene glycol maleimide) revealing that, with the exception of the lipoprotein anchor, the entire OPH is in the periplasmic space.
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Affiliation(s)
- Sunil Parthasarathy
- Department of Animal Sciences, School of Life Sciences, University of Hyderabad, C. R. Rao Road, Gachibowli, Hyderabad 500 046, India
| | - Hari Parapatla
- Department of Animal Sciences, School of Life Sciences, University of Hyderabad, C. R. Rao Road, Gachibowli, Hyderabad 500 046, India
| | - Dayananda Siddavattam
- Department of Animal Sciences, School of Life Sciences, University of Hyderabad, C. R. Rao Road, Gachibowli, Hyderabad 500 046, India
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125
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Membrane proteins structures: A review on computational modeling tools. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:2021-2039. [DOI: 10.1016/j.bbamem.2017.07.008] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 07/04/2017] [Accepted: 07/13/2017] [Indexed: 01/02/2023]
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126
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Wu H, Wang K, Lu L, Xue Y, Lyu Q, Jiang M. Deep Conditional Random Field Approach to Transmembrane Topology Prediction and Application to GPCR Three-Dimensional Structure Modeling. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2017; 14:1106-1114. [PMID: 27576262 DOI: 10.1109/tcbb.2016.2602872] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Transmembrane proteins play important roles in cellular energy production, signal transmission, and metabolism. Many shallow machine learning methods have been applied to transmembrane topology prediction, but the performance was limited by the large size of membrane proteins and the complex biological evolution information behind the sequence. In this paper, we proposed a novel deep approach based on conditional random fields named as dCRF-TM for predicting the topology of transmembrane proteins. Conditional random fields take into account more complicated interrelation between residue labels in full-length sequence than HMM and SVM-based methods. Three widely-used datasets were employed in the benchmark. DCRF-TM had the accuracy 95 percent over helix location prediction and the accuracy 78 percent over helix number prediction. DCRF-TM demonstrated a more robust performance on large size proteins (>350 residues) against 11 state-of-the-art predictors. Further dCRF-TM was applied to ab initio modeling three-dimensional structures of seven-transmembrane receptors, also known as G protein-coupled receptors. The predictions on 24 solved G protein-coupled receptors and unsolved vasopressin V2 receptor illustrated that dCRF-TM helped abGPCR-I-TASSER to improve TM-score 34.3 percent rather than using the random transmembrane definition. Two out of five predicted models caught the experimental verified disulfide bonds in vasopressin V2 receptor.
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127
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A membrane-inserted structural model of the yeast mitofusin Fzo1. Sci Rep 2017; 7:10217. [PMID: 28860650 PMCID: PMC5578988 DOI: 10.1038/s41598-017-10687-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 08/14/2017] [Indexed: 01/23/2023] Open
Abstract
Mitofusins are large transmembrane GTPases of the dynamin-related protein family, and are required for the tethering and fusion of mitochondrial outer membranes. Their full-length structures remain unknown, which is a limiting factor in the study of outer membrane fusion. We investigated the structure and dynamics of the yeast mitofusin Fzo1 through a hybrid computational and experimental approach, combining molecular modelling and all-atom molecular dynamics simulations in a lipid bilayer with site-directed mutagenesis and in vivo functional assays. The predicted architecture of Fzo1 improves upon the current domain annotation, with a precise description of the helical spans linked by flexible hinges, which are likely of functional significance. In vivo site-directed mutagenesis validates salient aspects of this model, notably, the long-distance contacts and residues participating in hinges. GDP is predicted to interact with Fzo1 through the G1 and G4 motifs of the GTPase domain. The model reveals structural determinants critical for protein function, including regions that may be involved in GTPase domain-dependent rearrangements.
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Jackson GE, Pavadai E, Gäde G, Timol Z, Andersen NH. Interaction of the red pigment-concentrating hormone of the crustacean Daphnia pulex, with its cognate receptor, Dappu-RPCHR: A nuclear magnetic resonance and modeling study. Int J Biol Macromol 2017; 106:969-978. [PMID: 28837848 DOI: 10.1016/j.ijbiomac.2017.08.103] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 08/14/2017] [Accepted: 08/16/2017] [Indexed: 11/17/2022]
Abstract
The primary sequence of the red pigment-concentrating hormone (RPCH) receptor of the water flea, Daphnia pulex, was used in homology modeling to construct the first 3D model of a crustacean G-protein coupled receptor, Dappu-RPCHR. This receptor was found to belong to the class A subfamily of GPCRs with a disulfide bridge between Cys72 and Cys150 and an ionic lock between Arg97 and Thr224 and Thr220. NMR restrained molecular dynamics was used to determine the structure of an agonist, Dappu-RPCH, in a membrane-mimicking environment. The agonist was found to be flexible but has two main conformations in solution, both having β-turns. Docking of the predominant structure was used to find a binding pocket on the receptor. The pocket's spatial location was similar to that of the AKH receptor of Anopheles gambiae. The binding affinity was -69kcalmol-1 with the N-terminus of Dappu-RPCH inserted between helices 4 and 6, and the C-terminus interacting with extra-cellular loop, ECL2. Upon binding, H-bonding to the peptide may activate the receptor. This development of the first Dappu-RPCH/Dappu-RPCHR model could be useful for understanding ligand-receptor interactions in crustaceans.
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Affiliation(s)
- Graham E Jackson
- Department of Chemistry, University of Cape Town, Private Bag, Rondebosch, Cape Town, 7701, South Africa.
| | - Elumalai Pavadai
- Department of Chemistry, University of Cape Town, Private Bag, Rondebosch, Cape Town, 7701, South Africa; Current address, Department of Physics, Florida International University, Miami, 33199, FL, United States
| | - Gerd Gäde
- Department of Biological Sciences, University of Cape Town, Private Bag, Rondebosch, Cape Town, 7701, South Africa
| | - Zaheer Timol
- Department of Chemistry, University of Cape Town, Private Bag, Rondebosch, Cape Town, 7701, South Africa
| | - Niels H Andersen
- Chemistry Department, University of Washington, Seattle, WA, 98195, United States
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Nielsen H. Predicting Subcellular Localization of Proteins by Bioinformatic Algorithms. Curr Top Microbiol Immunol 2017; 404:129-158. [PMID: 26728066 DOI: 10.1007/82_2015_5006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
When predicting the subcellular localization of proteins from their amino acid sequences, there are basically three approaches: signal-based, global property-based, and homology-based. Each of these has its advantages and drawbacks, and it is important when comparing methods to know which approach was used. Various statistical and machine learning algorithms are used with all three approaches, and various measures and standards are employed when reporting the performances of the developed methods. This chapter presents a number of available methods for prediction of sorting signals and subcellular localization, but rather than providing a checklist of which predictors to use, it aims to function as a guide for critical assessment of prediction methods.
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Affiliation(s)
- Henrik Nielsen
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Kemitorvet building 208, 2800, Lyngby, Denmark.
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130
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Computational studies of membrane proteins: from sequence to structure to simulation. Curr Opin Struct Biol 2017; 45:133-141. [DOI: 10.1016/j.sbi.2017.04.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 04/07/2017] [Accepted: 04/07/2017] [Indexed: 11/19/2022]
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131
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Li Y, Yang T, Dai D, Hu Y, Guo X, Guo H. Evolution, gene expression profiling and 3D modeling of CSLD proteins in cotton. BMC PLANT BIOLOGY 2017; 17:119. [PMID: 28693426 PMCID: PMC5504666 DOI: 10.1186/s12870-017-1063-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 06/25/2017] [Indexed: 05/12/2023]
Abstract
BACKGROUND Among CESA-like gene superfamily, the cellulose synthase-like D (CSLD) genes are most similar to cellulose synthase genes and have been reported to be involved in tip-growing cell and stem development. However, there has been no genome-wide characterization of this gene subfamily in cotton. We thus sought to analyze the evolution and functional characterization of CSLD proteins in cotton based on fully sequenced cotton genomes. RESULTS A total of 23 full-length CSLD proteins were identified in Gossypium raimondii, Gossypium arboreum and Gossypium hirsutum. The phylogenetic tree divided the CSLD proteins into five clades with strong support: CSLD1, CSLD2/3, CSLD4, CSLD5 and CSLD6. The total expression of GhCSLD genes was the highest in androecium & gynoecium (mostly contributed by CSLD1 and CSLD4) compared with other CSL genes. CSLD1 and CSLD4 were only highly expressed in androecium & gynoecium (A&G), and showed tissue-specific expression. The total expression of CSLD2/3, 5 and 6 was highest in the specific tissues. These results suggest that CSLD genes showed the different pattern of expression. Cotton CSLD proteins were subjected to different evolutionary pressures, and the CSLD1 and CSLD4 proteins exhibited episodic and long-term shift positive selection. The predicted three-dimensional structure of GrCSLD1 suggested that GrCSLD1 belongs to glycosyltransferase family 2. The amino acid residues under positive selection in the CSLD1 lineage are positioned in a region adjacent to the class-specific region (CSR), β1-strand and transmembrane helices (TMHs) in the GrCSLD1structure. CONCLUSION Our results characterized the CSLD proteins by an integrated approach containing phylogeny, transcriptional profiling and 3D modeling. The study added to the understanding about the importance of the CSLD family and provide a useful reference for selecting candidate genes and their associations with the biosynthesis of the cell wall in cotton.
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Affiliation(s)
- Yanpeng Li
- Industrial Crop Research Institute, Henan Academy of Agricultural Sciences, No. 116, Huayuan Road, Zhengzhou, 450002 China
- Scientific Observing and Experimental Station of Crop Cultivation in Central Plain, Ministry of Agriculture, No. 116, Huayuan Road, Zhengzhou, 450002 China
| | - Tiegang Yang
- Industrial Crop Research Institute, Henan Academy of Agricultural Sciences, No. 116, Huayuan Road, Zhengzhou, 450002 China
- Scientific Observing and Experimental Station of Crop Cultivation in Central Plain, Ministry of Agriculture, No. 116, Huayuan Road, Zhengzhou, 450002 China
| | - Dandan Dai
- Industrial Crop Research Institute, Henan Academy of Agricultural Sciences, No. 116, Huayuan Road, Zhengzhou, 450002 China
- Scientific Observing and Experimental Station of Crop Cultivation in Central Plain, Ministry of Agriculture, No. 116, Huayuan Road, Zhengzhou, 450002 China
| | - Ying Hu
- Industrial Crop Research Institute, Henan Academy of Agricultural Sciences, No. 116, Huayuan Road, Zhengzhou, 450002 China
- Scientific Observing and Experimental Station of Crop Cultivation in Central Plain, Ministry of Agriculture, No. 116, Huayuan Road, Zhengzhou, 450002 China
| | - Xiaoyang Guo
- Industrial Crop Research Institute, Henan Academy of Agricultural Sciences, No. 116, Huayuan Road, Zhengzhou, 450002 China
- Scientific Observing and Experimental Station of Crop Cultivation in Central Plain, Ministry of Agriculture, No. 116, Huayuan Road, Zhengzhou, 450002 China
| | - Hongxia Guo
- Industrial Crop Research Institute, Henan Academy of Agricultural Sciences, No. 116, Huayuan Road, Zhengzhou, 450002 China
- Scientific Observing and Experimental Station of Crop Cultivation in Central Plain, Ministry of Agriculture, No. 116, Huayuan Road, Zhengzhou, 450002 China
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Hughes DT, Pelletier J, Rahman S, Chen S, Leal WS, Luetje CW. Functional and Nonfunctional Forms of CquiOR91, an Odorant Selectivity Subunit of Culex quinquefasciatus. Chem Senses 2017; 42:333-341. [PMID: 28334229 DOI: 10.1093/chemse/bjx011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
In Culex quinquefasciatus, CquiOR91 is the ortholog of 2 larvae-specific odorant receptors (ORs) from Anopheles gambiae (Agam\Or40, previously shown to respond to several odorant ligands including the broad-spectrum repellent N,N-diethyl-3-methylbenzamide, DEET) and Aedes aegypti (Aaeg\Or40). When we cloned full-length CquiOR91 from a Culex quinquefasciatus larval head RNA sample, we found 2 alleles of this OR, differing at 9 residues. Functional analysis using the Xenopus oocyte expression system and 2-electrode voltage clamp electrophysiology revealed one allele (CquiOR91.1) to be nonfunctional, whereas the other allele (CquiOR91.2) was functional. Receptors formed by CquiOR91.2 and Cqui\Orco responded to (-)-fenchone, (+)-fenchone, and DEET, similar to what has been reported for Agam\Or40. We also identified 5 novel odorant ligands for the CquiOR91.2 + Cqui\Orco receptor: 2-isobutylthiazole, veratrole, eucalyptol, d-camphor, and safranal, with safranal being the most potent. To explore possible reasons for the lack of function for CquiOR91.1, we generated a series of mutant CquiOR91.2 subunits, in which the residue at each of the 9 polymorphic residue positions was changed from what occurs in CquiOR91.2 to what occurs in CquiOR91.1. Eight of the 9 mutant versions of CquiOR91.2 formed functional receptors, responding to (-)-fenchone. Only the CquiOR91.2 Y183C mutant was nonfunctional. The reverse mutation (C183Y) conferred function on CquiOR91.1 , which became responsive to (-)-fenchone and safranal. These results indicate that the "defect" in CquiOR91.1 that prevents function is the cysteine at position 183.
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Affiliation(s)
- David T Hughes
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, R-189, PO Box 016189, Miami, FL 33101, USA and.,Present address: Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Julien Pelletier
- Department of Molecular and Cellular Biology, University of California, 1 Shields Avenue, Davis, CA 95616, USA.,Present address: School of Life Sciences, Keele University, Keele, Staffordshire ST5 5BG, UK
| | - Suhaila Rahman
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, R-189, PO Box 016189, Miami, FL 33101, USA and
| | - Sisi Chen
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, R-189, PO Box 016189, Miami, FL 33101, USA and.,Present address: Leidos Biomedical Research, Inc., Rockville, MD 20892, USA
| | - Walter S Leal
- Department of Molecular and Cellular Biology, University of California, 1 Shields Avenue, Davis, CA 95616, USA
| | - Charles W Luetje
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, R-189, PO Box 016189, Miami, FL 33101, USA and
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Ribeiro AP, de Souza WR, Martins PK, Vinecky F, Duarte KE, Basso MF, da Cunha BADB, Campanha RB, de Oliveira PA, Centeno DC, Cançado GMA, de Magalhães JV, de Sousa CAF, Andrade AC, Kobayashi AK, Molinari HBC. Overexpression of BdMATE Gene Improves Aluminum Tolerance in Setaria viridis. FRONTIERS IN PLANT SCIENCE 2017; 8:865. [PMID: 28642761 PMCID: PMC5462932 DOI: 10.3389/fpls.2017.00865] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 05/09/2017] [Indexed: 05/02/2023]
Abstract
Acidic soils are distributed worldwide, predominantly in tropical and subtropical areas, reaching around 50% of the arable soil. This type of soil strongly reduces crop production, mainly because of the presence of aluminum, which has its solubility increased at low pH levels. A well-known physiological mechanism used by plants to cope with Al stress involves activation of membrane transporters responsible for organic acid anions secretion from the root apex to the rhizosphere, which chelate Al, preventing its absorption by roots. In sorghum, a membrane transporter gene belonging to multidrug and toxic compound extrusion (MATE) family was identified and characterized as an aluminum-activated citrate transporter gene responsible for Al tolerance in this crop. Setaria viridis is an emerging model for C4 species and it is an important model to validate some genes for further C4 crops transformation, such as sugarcane, maize, and wheat. In the present work, Setaria viridis was used as a model plant to overexpress a newly identified MATE gene from Brachypodium distachyon (BdMATE), closely related to SbMATE, for aluminum tolerance assays. Transgenic S. viridis plants overexpressing a BdMATE presented an improved Al tolerance phenotype, characterized by sustained root growth and exclusion of aluminum from the root apex in transgenic plants, as confirmed by hematoxylin assay. In addition, transgenic plants showed higher root citrate exudation into the rhizosphere, suggesting that Al tolerance improvement in these plants could be related to the chelation of the metal by the organic acid anion. These results suggest that BdMATE gene can be used to transform C4 crops of economic importance with improved aluminum tolerance.
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Affiliation(s)
- Ana P. Ribeiro
- Genetics and Biotechnology Laboratory, Embrapa AgroenergyBrasilia, Brazil
- Plant Biotechnology Program, Federal University of LavrasLavras, Brazil
| | - Wagner R. de Souza
- Genetics and Biotechnology Laboratory, Embrapa AgroenergyBrasilia, Brazil
| | - Polyana K. Martins
- Genetics and Biotechnology Laboratory, Embrapa AgroenergyBrasilia, Brazil
| | - Felipe Vinecky
- Genetics and Biotechnology Laboratory, Embrapa AgroenergyBrasilia, Brazil
| | - Karoline E. Duarte
- Genetics and Biotechnology Laboratory, Embrapa AgroenergyBrasilia, Brazil
| | - Marcos F. Basso
- Genetics and Biotechnology Laboratory, Embrapa AgroenergyBrasilia, Brazil
| | | | - Raquel B. Campanha
- Biomass and Biofuels Chemistry Laboratory, Embrapa AgroenergyBrasilia, Brazil
| | | | - Danilo C. Centeno
- Centre of Natural Sciences and Humanities, Federal University of ABCSão Bernardo do Campo, Brazil
| | - Geraldo M. A. Cançado
- Center of Genetic Engineering and Molecular Biology, Embrapa GenClima, University of Campinas, CampinasBrazil
| | | | | | - Alan C. Andrade
- Plant Biotechnology Program, Federal University of LavrasLavras, Brazil
- INOVACAFÉ, Embrapa CoffeeLavras, Brazil
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Loss of the Human Cytomegalovirus US16 Protein Abrogates Virus Entry into Endothelial and Epithelial Cells by Reducing the Virion Content of the Pentamer. J Virol 2017; 91:JVI.00205-17. [PMID: 28331097 DOI: 10.1128/jvi.00205-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 03/14/2017] [Indexed: 12/19/2022] Open
Abstract
The human cytomegalovirus (HCMV) US12 gene family encodes a group of predicted seven-transmembrane proteins whose functions have yet to be established. While inactivation of individual US12 members in laboratory strains of HCMV does not affect viral replication in fibroblasts, disruption of the US16 gene in the low-passage-number TR strain prevents viral growth in endothelial and epithelial cells. In these cells, the US16-null viruses fail to express immediate early (IE), early (E), and late (L) viral proteins due to a defect which occurs prior to IE gene expression. Here, we show that this defective phenotype is a direct consequence of deficiencies in the entry of US16-null viruses in these cell types due to an impact on the gH/gL/UL128/UL130/UL131A (pentamer) complex. Indeed, viral particles released from fibroblasts infected with US16-null viruses were defective for the pentamer, thus preventing entry during infections of endothelial and epithelial cells. A link between pUS16 and the pentamer was further supported by the colocalization of pUS16 and pentamer proteins within the cytoplasmic viral assembly compartment (cVAC) of infected fibroblasts. Deletion of the C-terminal tail of pUS16 reproduced the defective growth phenotype and alteration of virion composition as US16-null viruses. However, the pentamer assembly and trafficking to the cVAC were not affected by the lack of the C terminus of pUS16. Coimmunoprecipitation results then indicated that US16 interacts with pUL130 but not with the mature pentamer or gH/gL/gO. Together, these results suggest that pUS16 contributes to the tropism of HCMV by influencing the content of the pentamer into virions.IMPORTANCE Human cytomegalovirus (HCMV) is major pathogen in newborns and immunocompromised individuals. A hallmark of HCMV pathogenesis is its ability to productively replicate in an exceptionally broad range of target cells. The virus infects a variety of cell types by exploiting different forms of the envelope glycoprotein gH/gL hetero-oligomers, which allow entry into many cell types through different pathways. For example, incorporation of the pentameric gH/gL/UL128/UL130/UL131A complex into virions is a prerequisite for infection of endothelial and epithelial cells. Here, we show that the absence of US16, a thus far uncharacterized HCMV multitransmembrane protein, abrogates virus entry into endothelial and epithelial cells and that this defect is due to the lack of adequate amounts of the pentameric complex in extracellular viral particles. Our study suggests pUS16 as a novel viral regulatory protein important for shaping virion composition in a manner that influences HCMV cell tropism.
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Comparative study on secretome and transmembranome of immature and mature metacestodes of Echinococcus multilocularis. Vet Parasitol 2017. [PMID: 28637587 DOI: 10.1016/j.vetpar.2017.05.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Alveolar echinococcosis (AE) is a worldwide zoonosis caused by E. multilocularis. Humans become infected through oral ingestion of the eggs. Host of E. multilocularis produces immune responses that help to either reject and/or limit the growth of this parasite, and in response the parasite produces molecules against this immune attack. This study identifies candidate key molecules in the early infection phase and the chronic stage of the parasite infestation, through comparison of gene expression of 4- and 16-week metacestodes. First, RNA was isolated from 4- and 16-weeks metacestodes of E. multilocularis (Nemuro strain). Thereafter, clean reads with lengths of 50bp or longer were compared against a reference genome using TopHat. Functional annotation of transcripts of E. multilocularis were investigated using multi-step bioinformatics tools. At the gene ontology (GO) level, 356 and 1774 transmembrane (TM) predicted proteins of the E. multilocularis were mapped to an enhanced 'hydrolase activity' and increased 'transmembrane transporter activity', respectively. In addition, comparison of gene expression level between 4- and 16-week metacestode revealed 168 different expression (DE) genes. This study has demonstrated that, the expression levels of predicted ES and TM proteins in E. multilocularis change in the transformation from one stage to another. Genes that are highly expressed in immature or mature metacestode could be explored as novel candidates for diagnostic antigens and vaccine targets.
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136
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Liu Z, Lv H, Han J, Liu R. A computational model for predicting transmembrane regions of retroviruses. J Bioinform Comput Biol 2017; 15:1750010. [PMID: 28403667 DOI: 10.1142/s021972001750010x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Transmembrane region (TR) is a conserved region of transmembrane (TM) subunit in envelope (env) glycoprotein of retrovirus. Evidences have shown that TR is responsible for anchoring the env glycoprotein on the lipid bilayer and substitution of the TR for a covalently linked lipid anchor abrogates fusion. However, universal software could not achieve sufficient accuracy as TM in env also has several motifs such as signal peptide, fusion peptide and immunosuppressive domain composed largely of hydrophobic residues. In this paper, a support vector machine-based (SVM) model is proposed to identify TRs in retroviruses. Firstly, physicochemical and evolutionary information properties were extracted as original features. And then, the feature importance was analyzed by minimum Redundancy Maximum Relevance (mRMR) feature selection criterion. Our model achieved an Sn of 0.955, Sp of 0.998, ACC of 0.995, MCC of 0.954 using 10-fold cross-validation on the training dataset. These results suggest that the proposed model can be used to predict TRs in non-annotation retroviruses and 11917, 3344, 2, 289 and 6 new putative TRs were found in HERV, HIV, HTLV, SIV, MLV, respectively.
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Affiliation(s)
- Ze Liu
- 1 School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China
| | - Hongqiang Lv
- 1 School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China
| | - Jiuqiang Han
- 1 School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China
| | - Ruiling Liu
- 1 School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China
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137
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Zhang YZ, Shen HB. Signal-3L 2.0: A Hierarchical Mixture Model for Enhancing Protein Signal Peptide Prediction by Incorporating Residue-Domain Cross-Level Features. J Chem Inf Model 2017; 57:988-999. [PMID: 28298081 DOI: 10.1021/acs.jcim.6b00484] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Signal peptides play key roles in targeting and translocation of integral membrane proteins and secretory proteins. However, signal peptides present several challenges for automatic prediction methods. One challenge is that it is difficult to discriminate signal peptides from transmembrane helices, as both the H-region of the peptides and the transmembrane helices are hydrophobic. Another is that it is difficult to identify the cleavage site between signal peptides and mature proteins, as cleavage motifs or patterns are still unclear for most proteins. To solve these problems and further enhance automatic signal peptide recognition, we report a new Signal-3L 2.0 predictor. Our new model is constructed with a hierarchical protocol, where it first determines the existence of a signal peptide. For this, we propose a new residue-domain cross-level feature-driven approach, and we demonstrate that protein functional domain information is particularly useful for discriminating between the transmembrane helices and signal peptides as they perform different functions. Next, in order to accurately identify the unique signal peptide cleavage sites along the sequence, we designed a top-down approach where a subset of potential cleavage sites are screened using statistical learning rules, and then a final unique site is selected according to its evolution conservation score. Because this mixed approach utilizes both statistical learning and evolution analysis, it shows a strong capacity for recognizing cleavage sites. Signal-3L 2.0 has been benchmarked on multiple data sets, and the experimental results have demonstrated its accuracy. The online server is available at www.csbio.sjtu.edu.cn/bioinf/Signal-3L/ .
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Affiliation(s)
- Yi-Ze Zhang
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University , Shanghai, 200240, China.,Key Laboratory of System Control and Information Processing, Ministry of Education of China , Shanghai, 200240, China
| | - Hong-Bin Shen
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University , Shanghai, 200240, China.,Key Laboratory of System Control and Information Processing, Ministry of Education of China , Shanghai, 200240, China
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138
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Erhardt M, Wheatley P, Kim EA, Hirano T, Zhang Y, Sarkar MK, Hughes KT, Blair DF. Mechanism of type-III protein secretion: Regulation of FlhA conformation by a functionally critical charged-residue cluster. Mol Microbiol 2017; 104:234-249. [PMID: 28106310 DOI: 10.1111/mmi.13623] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/16/2017] [Indexed: 11/28/2022]
Abstract
The bacterial flagellum contains a specialized secretion apparatus in its base that pumps certain protein subunits through the growing structure to their sites of installation beyond the membrane. A related apparatus functions in the injectisomes of gram-negative pathogens to export virulence factors into host cells. This mode of protein export is termed type-III secretion (T3S). Details of the T3S mechanism are unclear. It is energized by the proton gradient; here, a mutational approach was used to identify proton-binding groups that might function in transport. Conserved proton-binding residues in all the membrane components were tested. The results identify residues R147, R154 and D158 of FlhA as most critical. These lie in a small, well-conserved cytoplasmic domain of FlhA, located between transmembrane segments 4 and 5. Two-hybrid experiments demonstrate self-interaction of the domain, and targeted cross-linking indicates that it forms a multimeric array. A mutation that mimics protonation of the key acidic residue (D158N) was shown to trigger a global conformational change that affects the other, larger cytoplasmic domain that interacts with the export cargo. The results are discussed in the framework of a transport model based on proton-actuated movements in the cytoplasmic domains of FlhA.
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Affiliation(s)
- Marc Erhardt
- Department of Biology, University of Utah, Salt Lake City, UT, 84112, USA.,Junior Research Group Infection Biology of Salmonella, Helmholtz Centre for Infection Research, Inhoffenstraβe 7, Braunschweig, 38124, Germany
| | - Paige Wheatley
- Department of Biology, University of Utah, Salt Lake City, UT, 84112, USA
| | - Eun A Kim
- Department of Biology, University of Utah, Salt Lake City, UT, 84112, USA
| | - Takanori Hirano
- Department of Biology, University of Utah, Salt Lake City, UT, 84112, USA.,Toshiba Medical Service Corporation, 1385 Shimoichigami, Otawara-shi, Tochigi, 324-8550, Japan
| | - Yang Zhang
- Department of Biology, University of Utah, Salt Lake City, UT, 84112, USA
| | | | - Kelly T Hughes
- Department of Biology, University of Utah, Salt Lake City, UT, 84112, USA
| | - David F Blair
- Department of Biology, University of Utah, Salt Lake City, UT, 84112, USA
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139
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Saidijam M, Azizpour S, Patching SG. Comprehensive analysis of the numbers, lengths and amino acid compositions of transmembrane helices in prokaryotic, eukaryotic and viral integral membrane proteins of high-resolution structure. J Biomol Struct Dyn 2017; 36:443-464. [PMID: 28150531 DOI: 10.1080/07391102.2017.1285725] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We report a comprehensive analysis of the numbers, lengths and amino acid compositions of transmembrane helices in 235 high-resolution structures of integral membrane proteins. The properties of 1551 transmembrane helices in the structures were compared with those obtained by analysis of the same amino acid sequences using topology prediction tools. Explanations for the 81 (5.2%) missing or additional transmembrane helices in the prediction results were identified. Main reasons for missing transmembrane helices were mis-identification of N-terminal signal peptides, breaks in α-helix conformation or charged residues in the middle of transmembrane helices and transmembrane helices with unusual amino acid composition. The main reason for additional transmembrane helices was mis-identification of amphipathic helices, extramembrane helices or hairpin re-entrant loops. Transmembrane helix length had an overall median of 24 residues and an average of 24.9 ± 7.0 residues and the most common length was 23 residues. The overall content of residues in transmembrane helices as a percentage of the full proteins had a median of 56.8% and an average of 55.7 ± 16.0%. Amino acid composition was analysed for the full proteins, transmembrane helices and extramembrane regions. Individual proteins or types of proteins with transmembrane helices containing extremes in contents of individual amino acids or combinations of amino acids with similar physicochemical properties were identified and linked to structure and/or function. In addition to overall median and average values, all results were analysed for proteins originating from different types of organism (prokaryotic, eukaryotic, viral) and for subgroups of receptors, channels, transporters and others.
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Affiliation(s)
- Massoud Saidijam
- a Department of Molecular Medicine and Genetics, Research Centre for Molecular Medicine, School of Medicine , Hamadan University of Medical Sciences , Hamadan , Iran
| | - Sonia Azizpour
- a Department of Molecular Medicine and Genetics, Research Centre for Molecular Medicine, School of Medicine , Hamadan University of Medical Sciences , Hamadan , Iran
| | - Simon G Patching
- b School of BioMedical Sciences and the Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds , UK
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140
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Aguilera-Pesantes D, Méndez MA. Structure and sequence based functional annotation of Zika virus NS2b protein: Computational insights. Biochem Biophys Res Commun 2017; 492:659-667. [PMID: 28188791 DOI: 10.1016/j.bbrc.2017.02.035] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 01/23/2017] [Accepted: 02/06/2017] [Indexed: 02/06/2023]
Abstract
While Zika virus (ZIKV) outbreaks are a growing concern for global health, a deep understanding about the virus is lacking. Here we report a contribution to the basic science on the virus- a detailed computational analysis of the non structural protein NS2b. This protein acts as a cofactor for the NS3 protease (NS3Pro) domain that is important on the viral life cycle, and is an interesting target for drug development. We found that ZIKV NS2b cofactor is highly similar to other virus within the Flavivirus genus, especially to West Nile Virus, suggesting that it is completely necessary for the protease complex activity. Furthermore, the ZIKV NS2b has an important role to the function and stability of the ZIKV NS3 protease domain even when presents a low conservation score. In addition, ZIKV NS2b is mostly rigid, which could imply a non dynamic nature in substrate recognition. Finally, by performing a computational alanine scanning mutagenesis, we found that residues Gly 52 and Asp 83 in the NS2b could be important in substrate recognition.
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Affiliation(s)
- Daniel Aguilera-Pesantes
- Universidad San Francisco de Quito, Instituto de Simulación Computacional (ISC-USFQ), Diego de Robles sn y Vía Interoceánica, 17-1200-841, Quito, Ecuador; Universidad San Francisco de Quito, Grupo de Química Computacional y Teórica, Diego de Robles sn y Vía Interoceánica, 17-1200-841, Quito, Ecuador
| | - Miguel A Méndez
- Universidad San Francisco de Quito, Instituto de Simulación Computacional (ISC-USFQ), Diego de Robles sn y Vía Interoceánica, 17-1200-841, Quito, Ecuador; Universidad San Francisco de Quito, Grupo de Química Computacional y Teórica, Diego de Robles sn y Vía Interoceánica, 17-1200-841, Quito, Ecuador; Universidad San Francisco de Quito, Escuela de Medicina, Colegio de Ciencias de la Salud (COCSA), Av. Interoceánica Km 12 ½; y Av. Florencia, 17-1200-841, Cumbayá, Quito, Ecuador.
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141
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Venko K, Roy Choudhury A, Novič M. Computational Approaches for Revealing the Structure of Membrane Transporters: Case Study on Bilitranslocase. Comput Struct Biotechnol J 2017; 15:232-242. [PMID: 28228927 PMCID: PMC5312651 DOI: 10.1016/j.csbj.2017.01.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 01/19/2017] [Accepted: 01/20/2017] [Indexed: 11/23/2022] Open
Abstract
The structural and functional details of transmembrane proteins are vastly underexplored, mostly due to experimental difficulties regarding their solubility and stability. Currently, the majority of transmembrane protein structures are still unknown and this present a huge experimental and computational challenge. Nowadays, thanks to X-ray crystallography or NMR spectroscopy over 3000 structures of membrane proteins have been solved, among them only a few hundred unique ones. Due to the vast biological and pharmaceutical interest in the elucidation of the structure and the functional mechanisms of transmembrane proteins, several computational methods have been developed to overcome the experimental gap. If combined with experimental data the computational information enables rapid, low cost and successful predictions of the molecular structure of unsolved proteins. The reliability of the predictions depends on the availability and accuracy of experimental data associated with structural information. In this review, the following methods are proposed for in silico structure elucidation: sequence-dependent predictions of transmembrane regions, predictions of transmembrane helix–helix interactions, helix arrangements in membrane models, and testing their stability with molecular dynamics simulations. We also demonstrate the usage of the computational methods listed above by proposing a model for the molecular structure of the transmembrane protein bilitranslocase. Bilitranslocase is bilirubin membrane transporter, which shares similar tissue distribution and functional properties with some of the members of the Organic Anion Transporter family and is the only member classified in the Bilirubin Transporter Family. Regarding its unique properties, bilitranslocase is a potentially interesting drug target.
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Affiliation(s)
- Katja Venko
- Department of Cheminformatics, National Institute of Chemistry, Ljubljana, Slovenia
| | - A Roy Choudhury
- Department of Cheminformatics, National Institute of Chemistry, Ljubljana, Slovenia
| | - Marjana Novič
- Department of Cheminformatics, National Institute of Chemistry, Ljubljana, Slovenia
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142
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Mourin M, Schubiger CB, Resch CT, Häse CC, Dibrov P. Physiology of the Vc-NhaP paralogous group of cation–proton antiporters in Vibrio cholerae. Mol Cell Biochem 2017; 428:87-99. [DOI: 10.1007/s11010-016-2919-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 12/21/2016] [Indexed: 10/20/2022]
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143
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Kuipers G, Peschke M, Ismail NB, Hjelm A, Schlegel S, Vikström D, Luirink J, de Gier JW. Optimizing E. coli-Based Membrane Protein Production Using Lemo21(DE3) or pReX and GFP-Fusions. Methods Mol Biol 2017; 1586:109-126. [PMID: 28470601 DOI: 10.1007/978-1-4939-6887-9_7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Optimizing the conditions for the production of membrane proteins in E. coli is usually a laborious and time-consuming process. Combining the Lemo21(DE3) strain or the pReX T7-based expression vector with membrane proteins C-terminally fused to Green Fluorescent Protein (GFP) greatly facilitates the optimization of membrane protein production yields. Both Lemo21(DE3) and pReX allow precise regulation of expression intensities of genes encoding membrane proteins, which is critical to identify the optimal production condition for a membrane protein. The use of GFP-fusions allows direct monitoring and visualization of membrane proteins at any stage during the production optimization process.
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Affiliation(s)
- Grietje Kuipers
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, Svante Arrhenius väg 16C, SE-106 91, Stockholm, Sweden
- Xbrane Biopharma AB, Banvaktsvägen 22, SE-171 48, Solna, Sweden
| | - Markus Peschke
- The Amsterdam Institute of Molecules, Medicines and Systems, VU University Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | | | - Anna Hjelm
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, Svante Arrhenius väg 16C, SE-106 91, Stockholm, Sweden
| | - Susan Schlegel
- Molecular Microbial Ecology, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, Überlandstrasse 133, 8600, Dübendorf, Switzerland
| | - David Vikström
- Xbrane Biopharma AB, Banvaktsvägen 22, SE-171 48, Solna, Sweden
| | - Joen Luirink
- The Amsterdam Institute of Molecules, Medicines and Systems, VU University Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | - Jan-Willem de Gier
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, Svante Arrhenius väg 16C, SE-106 91, Stockholm, Sweden.
- Xbrane Biopharma AB, Banvaktsvägen 22, SE-171 48, Solna, Sweden.
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144
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Christensen S, Grøftehauge MK, Byriel K, Huston WM, Furlong E, Heras B, Martin JL, McMahon RM. Structural and Biochemical Characterization of Chlamydia trachomatis DsbA Reveals a Cysteine-Rich and Weakly Oxidising Oxidoreductase. PLoS One 2016; 11:e0168485. [PMID: 28030602 PMCID: PMC5193440 DOI: 10.1371/journal.pone.0168485] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Accepted: 11/30/2016] [Indexed: 11/24/2022] Open
Abstract
The Gram negative bacteria Chlamydia trachomatis is an obligate intracellular human pathogen that can cause pelvic inflammatory disease, infertility and blinding trachoma. C. trachomatis encodes a homolog of the dithiol oxidoreductase DsbA. Bacterial DsbA proteins introduce disulfide bonds to folding proteins providing structural bracing for secreted virulence factors, consequently these proteins are potential targets for antimicrobial drugs. Despite sharing functional and structural characteristics, the DsbA enzymes studied to date vary widely in their redox character. In this study we show that the truncated soluble form of the predicted membrane anchored protein C. trachomatis DsbA (CtDsbA) has oxidase activity and redox properties broadly similar to other characterized DsbA proteins. However CtDsbA is distinguished from other DsbAs by having six cysteines, including a second disulfide bond, and an unusual dipeptide sequence in its catalytic motif (Cys-Ser-Ala-Cys). We report the 2.7 Å crystal structure of CtDsbA revealing a typical DsbA fold, which is most similar to that of DsbA-II type proteins. Consistent with this, the catalytic surface of CtDsbA is negatively charged and lacks the hydrophobic groove found in EcDsbA and DsbAs from other enterobacteriaceae. Biochemical characterization of CtDsbA reveals it to be weakly oxidizing compared to other DsbAs and with only a mildly destabilizing active site disulfide bond. Analysis of the crystal structure suggests that this redox character is consistent with a lack of contributing factors to stabilize the active site nucleophilic thiolate relative to more oxidizing DsbA proteins.
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Affiliation(s)
- Signe Christensen
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, St. Lucia, Queensland, Australia
| | - Morten K. Grøftehauge
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, St. Lucia, Queensland, Australia
| | - Karl Byriel
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, St. Lucia, Queensland, Australia
| | - Wilhelmina M. Huston
- School of Life Sciences, University of Technology Sydney, Broadway, New South Wales, Australia
| | - Emily Furlong
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, St. Lucia, Queensland, Australia
| | - Begoña Heras
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, St. Lucia, Queensland, Australia
| | - Jennifer L. Martin
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, St. Lucia, Queensland, Australia
- * E-mail: (JM); (RM)
| | - Róisín M. McMahon
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, St. Lucia, Queensland, Australia
- * E-mail: (JM); (RM)
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145
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Blondeau-Bidet E, Bossus M, Maugars G, Farcy E, Lignot JH, Lorin-Nebel C. Molecular characterization and expression of Na +/K +-ATPase α1 isoforms in the European sea bass Dicentrarchus labrax osmoregulatory tissues following salinity transfer. FISH PHYSIOLOGY AND BIOCHEMISTRY 2016; 42:1647-1664. [PMID: 27289588 DOI: 10.1007/s10695-016-0247-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 06/01/2016] [Indexed: 05/14/2023]
Abstract
The Na+/K+-ATPase (NKA) is considered as the main pump involved in active ion transport. In the European sea bass, Dicentrarchus labrax, we found two genes encoding for the alpha 1 subunit isoforms (NKA α1a and NKA α1b). NKA α1a and NKA α1b isoform amino acid (aa) sequences were compared through phylogeny and regarding key functional motifs between salmonids and other acanthomorph species. Analysis of aa sequences of both isoforms revealed a high degree of conservation across teleosts. The expression pattern of both nka α1a and nka α1b was measured in the gill, kidney and posterior intestine of fish in seawater (SW) and transferred to fresh water (FW) at different exposure times. Nka α1a was more expressed than nka α1b whatever the condition and the tissue analyzed. After long-term salinity acclimation (2.5 years) either in FW or SW, transcript levels of nka α1a were higher in the kidney followed by the posterior intestine and the gill. Compared to SW conditions, expression of nka α1a in FW was significantly increased or decreased, respectively, in gill and posterior intestine. In contrast, branchial nka α1b was significantly decreased in FW-acclimated fish. Short-term FW acclimation seems to rapidly increase nka α1a transcript levels in the kidney unlike in gill tissues where different gene expression levels are detected only after long-term acclimation.
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Affiliation(s)
- Eva Blondeau-Bidet
- Adaptation Ecophysiologique et Ontogenèse (AEO, UMR 9190 MARBEC), Université de Montpellier, Place Eugène Bataillon - CC092, 34095, Montpellier Cedex 5, France
| | - Maryline Bossus
- Adaptation Ecophysiologique et Ontogenèse (AEO, UMR 9190 MARBEC), Université de Montpellier, Place Eugène Bataillon - CC092, 34095, Montpellier Cedex 5, France
| | - Gersende Maugars
- Unité Biologie des Organismes et écosystèmes aquatiques (BOREA, UMR 7208), CNRS, IRD 207, Sorbonne Universités, Muséum national d'Histoire naturelle, Université Pierre et Marie Curie, Université de Caen Basse Normandie, CP32, 7 rue Cuvier, 75005, Paris, France
| | - Emilie Farcy
- Adaptation Ecophysiologique et Ontogenèse (AEO, UMR 9190 MARBEC), Université de Montpellier, Place Eugène Bataillon - CC092, 34095, Montpellier Cedex 5, France
| | - Jehan-Hervé Lignot
- Adaptation Ecophysiologique et Ontogenèse (AEO, UMR 9190 MARBEC), Université de Montpellier, Place Eugène Bataillon - CC092, 34095, Montpellier Cedex 5, France
| | - Catherine Lorin-Nebel
- Adaptation Ecophysiologique et Ontogenèse (AEO, UMR 9190 MARBEC), Université de Montpellier, Place Eugène Bataillon - CC092, 34095, Montpellier Cedex 5, France.
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146
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Taylor WR, Matthews-Palmer TRS, Beeby M. Molecular Models for the Core Components of the Flagellar Type-III Secretion Complex. PLoS One 2016; 11:e0164047. [PMID: 27855178 PMCID: PMC5113899 DOI: 10.1371/journal.pone.0164047] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 09/19/2016] [Indexed: 01/10/2023] Open
Abstract
We show that by using a combination of computational methods, consistent three-dimensional molecular models can be proposed for the core proteins of the type-III secretion system. We employed a variety of approaches to reconcile disparate, and sometimes inconsistent, data sources into a coherent picture that for most of the proteins indicated a unique solution to the constraints. The range of difficulty spanned from the trivial (FliQ) to the difficult (FlhA and FliP). The uncertainties encountered with FlhA were largely the result of the greater number of helix packing possibilities allowed in a large protein, however, for FliP, there remains an uncertainty in how to reconcile the large displacement predicted between its two main helical hairpins and their ability to sit together happily across the bacterial membrane. As there is still no high resolution structural information on any of these proteins, we hope our predicted models may be of some use in aiding the interpretation of electron microscope images and in rationalising mutation data and experiments.
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Affiliation(s)
- William R. Taylor
- Laboratory of Computational Cell and Molecular Biology, Francis Crick Institute, 1 Midland Rd., London NW1 1AT, United Kingdom
| | - Teige R. S. Matthews-Palmer
- Laboratory of Computational Cell and Molecular Biology, Francis Crick Institute, 1 Midland Rd., London NW1 1AT, United Kingdom
- Department of Life Sciences, Imperial College, London, United Kingdom
| | - Morgan Beeby
- Department of Life Sciences, Imperial College, London, United Kingdom
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147
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Truong HH, Kim BL, Schafer NP, Wolynes PG. Predictive energy landscapes for folding membrane protein assemblies. J Chem Phys 2016; 143:243101. [PMID: 26723586 DOI: 10.1063/1.4929598] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We study the energy landscapes for membrane protein oligomerization using the Associative memory, Water mediated, Structure and Energy Model with an implicit membrane potential (AWSEM-membrane), a coarse-grained molecular dynamics model previously optimized under the assumption that the energy landscapes for folding α-helical membrane protein monomers are funneled once their native topology within the membrane is established. In this study we show that the AWSEM-membrane force field is able to sample near native binding interfaces of several oligomeric systems. By predicting candidate structures using simulated annealing, we further show that degeneracies in predicting structures of membrane protein monomers are generally resolved in the folding of the higher order assemblies as is the case in the assemblies of both nicotinic acetylcholine receptor and V-type Na(+)-ATPase dimers. The physics of the phenomenon resembles domain swapping, which is consistent with the landscape following the principle of minimal frustration. We revisit also the classic Khorana study of the reconstitution of bacteriorhodopsin from its fragments, which is the close analogue of the early Anfinsen experiment on globular proteins. Here, we show the retinal cofactor likely plays a major role in selecting the final functional assembly.
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Affiliation(s)
- Ha H Truong
- Department of Chemistry, Rice University, Houston, Texas 77005, USA
| | - Bobby L Kim
- Department of Chemistry, Rice University, Houston, Texas 77005, USA
| | - Nicholas P Schafer
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, USA
| | - Peter G Wolynes
- Department of Chemistry, Rice University, Houston, Texas 77005, USA
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148
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Bernhofer M, Kloppmann E, Reeb J, Rost B. TMSEG: Novel prediction of transmembrane helices. Proteins 2016; 84:1706-1716. [PMID: 27566436 DOI: 10.1002/prot.25155] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Revised: 07/18/2016] [Accepted: 08/24/2016] [Indexed: 12/15/2022]
Abstract
Transmembrane proteins (TMPs) are important drug targets because they are essential for signaling, regulation, and transport. Despite important breakthroughs, experimental structure determination remains challenging for TMPs. Various methods have bridged the gap by predicting transmembrane helices (TMHs), but room for improvement remains. Here, we present TMSEG, a novel method identifying TMPs and accurately predicting their TMHs and their topology. The method combines machine learning with empirical filters. Testing it on a non-redundant dataset of 41 TMPs and 285 soluble proteins, and applying strict performance measures, TMSEG outperformed the state-of-the-art in our hands. TMSEG correctly distinguished helical TMPs from other proteins with a sensitivity of 98 ± 2% and a false positive rate as low as 3 ± 1%. Individual TMHs were predicted with a precision of 87 ± 3% and recall of 84 ± 3%. Furthermore, in 63 ± 6% of helical TMPs the placement of all TMHs and their inside/outside topology was correctly predicted. There are two main features that distinguish TMSEG from other methods. First, the errors in finding all helical TMPs in an organism are significantly reduced. For example, in human this leads to 200 and 1600 fewer misclassifications compared to the second and third best method available, and 4400 fewer mistakes than by a simple hydrophobicity-based method. Second, TMSEG provides an add-on improvement for any existing method to benefit from. Proteins 2016; 84:1706-1716. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Michael Bernhofer
- Department of Informatics & Center for Bioinformatics & Computational Biology - i12, Technische Universität München (TUM), Boltzmannstr. 3, Garching/Munich, 85748, Germany.
| | - Edda Kloppmann
- Department of Informatics & Center for Bioinformatics & Computational Biology - i12, Technische Universität München (TUM), Boltzmannstr. 3, Garching/Munich, 85748, Germany.,New York Consortium on Membrane Protein Structure, New York Structural Biology Center, New York, New York, 10027
| | - Jonas Reeb
- Department of Informatics & Center for Bioinformatics & Computational Biology - i12, Technische Universität München (TUM), Boltzmannstr. 3, Garching/Munich, 85748, Germany
| | - Burkhard Rost
- Department of Informatics & Center for Bioinformatics & Computational Biology - i12, Technische Universität München (TUM), Boltzmannstr. 3, Garching/Munich, 85748, Germany.,New York Consortium on Membrane Protein Structure, New York Structural Biology Center, New York, New York, 10027.,Institute of Advanced Study (TUM-IAS), Lichtenbergstr. 2a, Garching/Munich, 85748, Germany.,Institute for Food and Plant Sciences WZW - Weihenstephan, Alte Akademie 8, Freising, Germany
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149
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The role of receptor topology in the vitamin D3 uptake and Ca 2+ response systems. Biochem Biophys Res Commun 2016; 477:834-840. [DOI: 10.1016/j.bbrc.2016.06.143] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 06/27/2016] [Indexed: 11/18/2022]
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150
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Taylor WR. Reduction, alignment and visualisation of large diverse sequence families. BMC Bioinformatics 2016; 17:300. [PMID: 27484804 PMCID: PMC4971687 DOI: 10.1186/s12859-016-1059-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 04/21/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Current volumes of sequence data can lead to large numbers of hits identified on a search, typically in the range of 10s to 100s of thousands. It is often quite difficult to tell from these raw results whether the search has been a success or has picked-up sequences with little or no relationship to the query. The best approach to this problem is to cluster and align the resulting families, however, existing methods concentrate on fast clustering and either do not align the sequences or only perform a limited alignment. RESULTS A method (MULSEL) is presented that combines fast peptide-based pre-sorting with a following cascade of mini-alignments, each of which are generated with a robust profile/profile method. From these mini-alignments, a representative sequence is selected, based on a variety of intrinsic and user-specified criteria that are combined to produce the sequence collection for the next cycle of alignment. For moderate sized sequence collections (10s of thousands) the method executes on a laptop computer within seconds or minutes. CONCLUSIONS MULSEL bridges a gap between fast clustering methods and slower multiple sequence alignment methods and provides a seamless transition from one to the other. Furthermore, it presents the resulting reduced family in a graphical manner that makes it clear if family members have been misaligned or if there are sequences present that appear inconsistent.
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