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Dong CS, Zhang WL, Wang XY, Wang X, Wang J, Wang M, Fang Y, Liu L. Crystallographic and functional studies of a plant temperature-induced lipocalin. Biochim Biophys Acta Gen Subj 2024; 1868:130540. [PMID: 38103756 DOI: 10.1016/j.bbagen.2023.130540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/30/2023] [Accepted: 12/09/2023] [Indexed: 12/19/2023]
Abstract
Arabidopsis thaliana temperature-induced lipocalin (AtTIL) is a prototypical member of plant lipocalins and participates in a variety of cellular processes, particularly stress responses. Bioinformatical and physiological studies have proposed its promiscuous ligand-binding ability, but the molecular basis is yet unclear. Here, we report the 1.9-Å crystal structure of AtTIL in complex with heme. Spectrophotometric absorbance titration with heme yields a dissociation constant of ∼2 micromolar, indicating the relatively weak interaction between AtTIL and heme, which is confirmed by the AtTIL-heme structure. Although binding to retinal or biliverdin is not detected, such possibility can not be precluded as suggested by comparison with other lipocalin structures. These results show that AtTIL is a structural and functional homolog of the bacterial lipocalin Blc.
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Affiliation(s)
- Chen-Song Dong
- School of Life Sciences, Anhui University, Hefei, Anhui 230601, China
| | - Wei-Lun Zhang
- School of Life Sciences, Anhui University, Hefei, Anhui 230601, China
| | - Xiao-Ying Wang
- School of Life Sciences, Anhui University, Hefei, Anhui 230601, China
| | - Xiao Wang
- School of Life Sciences, Anhui University, Hefei, Anhui 230601, China
| | - Jia Wang
- School of Life Sciences, Anhui University, Hefei, Anhui 230601, China
| | - Mingzhu Wang
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China
| | - Ying Fang
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Lin Liu
- School of Life Sciences, Anhui University, Hefei, Anhui 230601, China.
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2
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Diez-Hermano S, Ganfornina MD, Skerra A, Gutiérrez G, Sanchez D. An Evolutionary Perspective of the Lipocalin Protein Family. Front Physiol 2021; 12:718983. [PMID: 34497539 PMCID: PMC8420045 DOI: 10.3389/fphys.2021.718983] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 07/22/2021] [Indexed: 11/13/2022] Open
Abstract
The protein family of Lipocalins is ubiquitously present throughout the tree of life, with the exception of the phylum Archaea. Phylogenetic relationships of chordate Lipocalins have been proposed in the past based on protein sequence similarities, but their highly divergent primary structures and a shortage of experimental annotations in genome projects have precluded a well-supported hypothesis for their evolution. In this work we propose a novel topology for the phylogenetic tree of chordate Lipocalins, inferred from multiple amino acid sequence alignments. Sixteen jawed vertebrates with fair coverage by genomic sequencing were compared. The selected species span an evolutionary range of ∼400 million years, allowing for a balanced representation of all major vertebrate clades. A consensus phylogenetic tree is proposed following a comparison of sequence-based maximum-likelihood trees and protein structure dendrograms. This new phylogeny suggests an APOD-like common ancestor in early chordates, which gave rise, via whole-genome or tandem duplications, to the six Lipocalins currently present in fish (APOD, RBP4, PTGDS, AMBP, C8G, and APOM). Further gene duplications of APOM and PTGDS resulted in the altogether 15 Lipocalins found in contemporary mammals. Insights into the functional impact of relevant amino acid residues in early diverging Lipocalins are also discussed. These results should foster the experimental exploration of novel functions alongside the identification of new members of the Lipocalin family.
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Affiliation(s)
- Sergio Diez-Hermano
- Departamento de Bioquimica y Biologia Moleculary Fisiologia, Instituto de Biologia y Genetica Molecular, Universidad de Valladolid-Consejo Superior de Investigaciones Cientificas (CSIC), Valladolid, Spain
| | - Maria D Ganfornina
- Departamento de Bioquimica y Biologia Moleculary Fisiologia, Instituto de Biologia y Genetica Molecular, Universidad de Valladolid-Consejo Superior de Investigaciones Cientificas (CSIC), Valladolid, Spain
| | - Arne Skerra
- Lehrstuhl für Biologische Chemie, Technische Universität München, Freising, Germany
| | | | - Diego Sanchez
- Departamento de Bioquimica y Biologia Moleculary Fisiologia, Instituto de Biologia y Genetica Molecular, Universidad de Valladolid-Consejo Superior de Investigaciones Cientificas (CSIC), Valladolid, Spain
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3
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Ruiz M. Into the Labyrinth of the Lipocalin α1-Acid Glycoprotein. Front Physiol 2021; 12:686251. [PMID: 34168570 PMCID: PMC8217824 DOI: 10.3389/fphys.2021.686251] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/17/2021] [Indexed: 12/28/2022] Open
Abstract
α1-acid glycoprotein (AGP), also known as Orosomucoid (ORM), belongs to the Lipocalin protein family and it is well-known for being a positive acute-phase protein. AGP is mostly found in plasma, with the liver as main contributor, but it is also expressed in other tissues such as the brain or the adipose tissue. Despite the vast literature on AGP, the physiological functions of the protein remain to be elucidated. A large number of activities mostly related to protection and immune system modulation have been described. Recently created AGP-knockout models have suggested novel physiological roles of AGP, including regulation of metabolism. AGP has an outstanding ability to efficiently bind endogenous and exogenous small molecules that together with the complex and variable glycosylation patterns, determine AGP functions. This review summarizes and discusses the recent findings on AGP structure (including glycans), ligand-binding ability, regulation, and physiological functions of AGP. Moreover, this review explores possible molecular and functional connections between AGP and other members of the Lipocalin protein family.
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Affiliation(s)
- Mario Ruiz
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
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4
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Sawyer L. β-Lactoglobulin and Glycodelin: Two Sides of the Same Coin? Front Physiol 2021; 12:678080. [PMID: 34093238 PMCID: PMC8173191 DOI: 10.3389/fphys.2021.678080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 04/14/2021] [Indexed: 12/22/2022] Open
Abstract
The two lipocalins, β-lactoglobulin (βLg) and glycodelin (Gd), are possibly the most closely related members of the large and widely distributed lipocalin family, yet their functions appear to be substantially different. Indeed, the function of β-lactoglobulin, a major component of ruminant milk, is still unclear although neonatal nutrition is clearly important. On the other hand, glycodelin has several specific functions in reproduction conferred through distinct, tissue specific glycosylation of the polypeptide backbone. It is also associated with some cancer outcomes. The glycodelin gene, PAEP, reflecting one of its names, progestagen-associated endometrial protein, is expressed in many though not all primates, but the name has now also been adopted for the β-lactoglobulin gene (HGNC, www.genenames.org). After a general overview of the two proteins in the context of the lipocalin family, this review considers the properties of each in the light of their physiological functional significance, supplementing earlier reviews to include studies from the past decade. While the biological function of glycodelin is reasonably well defined, that of β-lactoglobulin remains elusive.
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Affiliation(s)
- Lindsay Sawyer
- School of Biological Sciences, IQB3, The University of Edinburgh, Edinburgh, United Kingdom
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5
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Kato-Unoki Y, Takai Y, Nagano Y, Matsunaga S, Enoki S, Takamura T, Kim S, Kinoshita M, Kitano T, Shimasaki Y, Oshima Y. Production of a tributyltin-binding protein 2 knockout mutant strain of Japanese medaka, Oryzias latipes. MARINE POLLUTION BULLETIN 2020; 160:111601. [PMID: 32871435 DOI: 10.1016/j.marpolbul.2020.111601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 08/22/2020] [Accepted: 08/23/2020] [Indexed: 06/11/2023]
Abstract
Tributyltin-binding proteins (TBT-bps), members of the lipocalin family, bind TBT in fish blood and are presumed to contribute to detoxification of TBT. Recent studies have shown that many fish species have TBT-bp genes, and that these genes are induced by stresses such as exposure to chemicals or fish pathogenic bacteria. However, the function of TBT-bps, and the mechanisms of their induction and detoxification activity are still unclear. Here, towards elucidating the functions of TBT-bp2, we produced a TBT-bp2 knockout (TBT-bp2-/-) strain of Japanese medaka, Oryzias latipes, by using the CRISPR/Cas9 system. Gene expression of the mutated TBT-bp2 was reduced, and the cDNA sequencing and predicted protein structure suggested possible loss of function. However, the fish could be grown under normal conditions. Exposure of the TBT-bp2-/- strain of medaka to various stresses in future experiments is expected to contribute to our understanding of this novel detoxification system in aquatic organisms.
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Affiliation(s)
- Yoko Kato-Unoki
- Center for Advanced Instrumental and Educational Supports, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Yuki Takai
- Laboratory of Marine Environmental Science, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Yosuke Nagano
- Laboratory of Marine Environmental Science, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Satoshi Matsunaga
- Laboratory of Marine Environmental Science, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Shintaro Enoki
- Laboratory of Marine Environmental Science, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Takumi Takamura
- Laboratory of Marine Environmental Science, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan; Chemicals Evaluation and Research Institute, Japan, 3-2-7, Miyanojin, Kurume-shi, Fukuoka 839-0801, Japan
| | - Sangwan Kim
- Laboratory of Molecular Gene Technology, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Masato Kinoshita
- Department of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Takeshi Kitano
- Department of Biological Sciences, Graduate School of Science and Technology, Kumamoto University, Kumamoto 860-8555, Japan
| | - Yohei Shimasaki
- Laboratory of Marine Environmental Science, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Yuji Oshima
- Laboratory of Marine Environmental Science, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan; Institute of Nature and Environmental Technology, Kanazawa University, Kanazawa 920-1192, Japan.
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Takai Y, Mizoguchi N, Kinoshita M, Qiu X, Shimasaki Y, Oshima Y. Establishment of a Japanese medaka (Oryzias latipes) transgenic line expressing Takifugu rubripes pufferfish saxitoxin and tetrodotoxin binding protein 1, and evaluation of tributyltin toxicity via in ovo nanoinjection. Comp Biochem Physiol C Toxicol Pharmacol 2020; 234:108785. [PMID: 32376496 DOI: 10.1016/j.cbpc.2020.108785] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 04/25/2020] [Accepted: 04/28/2020] [Indexed: 12/27/2022]
Abstract
Pufferfish saxitoxin and tetrodotoxin binding proteins (PSTBPs) play an important role in the toxification of certain species of pufferfish. Recombinant Takifugu rubripes PSTBP1 (rTrub.PSTBP1) is reported to bind to tributyltin, and so it has been suggested that rTrub.PSTBP1 may reduce the toxicity of tributyltin. However, the role of PSTBP1 in vivo remains to be elucidated. Here, we established a transgenic medaka line showing whole-body Renilla reniformis green fluorescent protein and Trub.PSTBP1 expression, as confirmed by real-time polymerase chain reaction and mRNA-Seq analysis. mRNA-Seq analysis also showed that cytochrome P450 superfamily genes and the gene encoding ATP-binding cassette sub-family G member 2 were highly expressed in the transgenic medaka. Using embryos of the transgenic medaka line, we conducted an in ovo nanoinjection test to examine the effect of Trub.PSTBP1 in vivo, and obtained data suggesting that Trub.PSTBP1 expression may have reduced the toxicity of tributyltin in our transgenic medaka line. Our findings will be useful for future functional analyses of Trub.PSTBP1.
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Affiliation(s)
- Yuki Takai
- Laboratory of Marine Environmental Science, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Naohiro Mizoguchi
- Laboratory of Marine Environmental Science, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Masato Kinoshita
- Department of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Xuchun Qiu
- Institute of Environmental Health and Ecological Security, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, PR China
| | - Yohei Shimasaki
- Laboratory of Marine Environmental Science, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Yuji Oshima
- Laboratory of Marine Environmental Science, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan; Institute of Nature and Environmental Technology, Kanazawa University, Kanazawa 920-1192, Japan.
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7
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Kato-Unoki Y, Takai Y, Kinoshita M, Mochizuki T, Tatsuno R, Shimasaki Y, Oshima Y. Genome editing of pufferfish saxitoxin- and tetrodotoxin-binding protein type 2 in Takifugu rubripes. Toxicon 2018; 153:58-61. [PMID: 30170168 DOI: 10.1016/j.toxicon.2018.08.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 08/03/2018] [Accepted: 08/19/2018] [Indexed: 01/17/2023]
Abstract
The pufferfish saxitoxin- and tetrodotoxin-binding protein 2 (PSTBP2), which is involved in toxin accumulation, was knocked out in Takifugu rubripes embryos by using clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 genome-editing technology. Treating the embryos with one of two single-guide RNA (sgRNA) resulted in mutation rates of 57.1% and 62.5%, respectively, as estimated using a heteroduplex mobility assay at 3 days postfertilization. Both sgRNAs might induced frameshift mutations that knocked out the T. rubripes PSTBP2.
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Affiliation(s)
- Yoko Kato-Unoki
- Laboratory of Marine Environmental Science, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Yuki Takai
- Laboratory of Marine Environmental Science, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Masato Kinoshita
- Department of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | | | - Ryohei Tatsuno
- Department of Food Science and Technology, National Fisheries University, Japan Fisheries Research and Education Agency, 2-7-1 Nagata-Honmachi, Shimonoseki, Yamaguchi 759-6595, Japan
| | - Yohei Shimasaki
- Laboratory of Marine Environmental Science, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Yuji Oshima
- Laboratory of Marine Environmental Science, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan.
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8
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Valdés JJ, Cabezas-Cruz A, Sima R, Butterill PT, Růžek D, Nuttall PA. Substrate prediction of Ixodes ricinus salivary lipocalins differentially expressed during Borrelia afzelii infection. Sci Rep 2016; 6:32372. [PMID: 27584086 PMCID: PMC5008119 DOI: 10.1038/srep32372] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 08/05/2016] [Indexed: 11/13/2022] Open
Abstract
Evolution has provided ticks with an arsenal of bioactive saliva molecules that counteract host defense mechanisms. This salivary pharmacopoeia enables blood-feeding while enabling pathogen transmission. High-throughput sequencing of tick salivary glands has thus become a major focus, revealing large expansion within protein encoding gene families. Among these are lipocalins, ubiquitous barrel-shaped proteins that sequester small, typically hydrophobic molecules. This study was initiated by mining the Ixodes ricinus salivary gland transcriptome for specific, uncharacterized lipocalins: three were identified. Differential expression of these I. ricinus lipocalins during feeding at distinct developmental stages and in response to Borrelia afzelii infection suggests a role in transmission of this Lyme disease spirochete. A phylogenetic analysis using 803 sequences places the three I. ricinus lipocalins with tick lipocalins that sequester monoamines, leukotrienes and fatty acids. Both structural analysis and biophysical simulations generated robust predictions showing these I. ricinus lipocalins have the potential to bind monoamines similar to other tick species previously reported. The multidisciplinary approach employed in this study characterized unique lipocalins that play a role in tick blood-feeding and transmission of the most important tick-borne pathogen in North America and Eurasia.
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Affiliation(s)
- James J Valdés
- Institute of Parasitology, The Czech Academy of Sciences, Branišovská 31, CZ-37005 České Budějovice, Czech Republic.,Department of Virology, Veterinary Research Institute, Hudcova 70, CZ-62100 Brno, Czech Republic
| | - Alejandro Cabezas-Cruz
- Center for Infection and Immunity of Lille (CIIL), INSERM U1019 - CNRS UMR 8204, Université Lille Nord de France, Institut Pasteur de Lille, Lille, France
| | - Radek Sima
- Institute of Parasitology, The Czech Academy of Sciences, Branišovská 31, CZ-37005 České Budějovice, Czech Republic
| | - Philip T Butterill
- Biology Center, The Czech Academy of Sciences, University of South Bohemia, Branišovská 31, CZ-37005 České Budějovice, Czech Republic
| | - Daniel Růžek
- Institute of Parasitology, The Czech Academy of Sciences, Branišovská 31, CZ-37005 České Budějovice, Czech Republic.,Department of Virology, Veterinary Research Institute, Hudcova 70, CZ-62100 Brno, Czech Republic.,Biology Center, The Czech Academy of Sciences, University of South Bohemia, Branišovská 31, CZ-37005 České Budějovice, Czech Republic
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9
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Lakshmi B, Mishra M, Srinivasan N, Archunan G. Structure-Based Phylogenetic Analysis of the Lipocalin Superfamily. PLoS One 2015; 10:e0135507. [PMID: 26263546 PMCID: PMC4532494 DOI: 10.1371/journal.pone.0135507] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 07/22/2015] [Indexed: 01/26/2023] Open
Abstract
Lipocalins constitute a superfamily of extracellular proteins that are found in all three kingdoms of life. Although very divergent in their sequences and functions, they show remarkable similarity in 3-D structures. Lipocalins bind and transport small hydrophobic molecules. Earlier sequence-based phylogenetic studies of lipocalins highlighted that they have a long evolutionary history. However the molecular and structural basis of their functional diversity is not completely understood. The main objective of the present study is to understand functional diversity of the lipocalins using a structure-based phylogenetic approach. The present study with 39 protein domains from the lipocalin superfamily suggests that the clusters of lipocalins obtained by structure-based phylogeny correspond well with the functional diversity. The detailed analysis on each of the clusters and sub-clusters reveals that the 39 lipocalin domains cluster based on their mode of ligand binding though the clustering was performed on the basis of gross domain structure. The outliers in the phylogenetic tree are often from single member families. Also structure-based phylogenetic approach has provided pointers to assign putative function for the domains of unknown function in lipocalin family. The approach employed in the present study can be used in the future for the functional identification of new lipocalin proteins and may be extended to other protein families where members show poor sequence similarity but high structural similarity.
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Affiliation(s)
- Balasubramanian Lakshmi
- Department of Animal Science, Bharathidasan University, Tiruchirappalli, 620024, India
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
| | - Madhulika Mishra
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Narayanaswamy Srinivasan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
- * E-mail: (NS); (GA)
| | - Govindaraju Archunan
- Department of Animal Science, Bharathidasan University, Tiruchirappalli, 620024, India
- * E-mail: (NS); (GA)
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10
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Du ZP, Wu BL, Wu X, Lin XH, Qiu XY, Zhan XF, Wang SH, Shen JH, Zheng CP, Wu ZY, Xu LY, Wang D, Li EM. A systematic analysis of human lipocalin family and its expression in esophageal carcinoma. Sci Rep 2015; 5:12010. [PMID: 26131602 PMCID: PMC4487233 DOI: 10.1038/srep12010] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 06/11/2015] [Indexed: 02/05/2023] Open
Abstract
The lipocalin proteins (lipocalins) are a large family of small proteins characterized by low sequence similarity and highly conserved crystal structures. Lipocalins have been found to play important roles in many human diseases. For this reason, a systemic analysis of the molecular properties of human lipocalins is essential. In this study, human lipocalins were found to contain four structurally conserved regions (SCRs) and could be divided into two subgroups. A human lipocalin protein-protein interaction network (PPIN) was constructed and integrated with their expression data in esophageal carcinoma. Many lipocalins showed obvious co-expression patterns in esophageal carcinoma. Their subcellular distributions also suggested these lipocalins may transfer signals from the extracellular space to the nucleus using the pathway-like paths. These analyses also expanded our knowledge about this human ancient protein family in the background of esophageal carcinoma.
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Affiliation(s)
- Ze-Peng Du
- Department of Pathology, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-sen University, Shantou 515041, China
| | - Bing-Li Wu
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, China
| | - Xuan Wu
- Department of Pathology, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-sen University, Shantou 515041, China
| | - Xuan-Hao Lin
- Department of Pathology, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-sen University, Shantou 515041, China
| | - Xiao-Yang Qiu
- Department of Pathology, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-sen University, Shantou 515041, China
| | - Xiao-Fen Zhan
- Department of Pathology, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-sen University, Shantou 515041, China
| | - Shao-Hong Wang
- Department of Pathology, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-sen University, Shantou 515041, China
| | - Jin-Hui Shen
- Department of Pathology, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-sen University, Shantou 515041, China
| | - Chun-Peng Zheng
- Department of Oncology Surgery, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-sen University, Shantou 515041, China
| | - Zhi-Yong Wu
- Department of Oncology Surgery, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-sen University, Shantou 515041, China
| | - Li-Yan Xu
- Institute of Oncologic Pathology, Shantou University Medical College, Shantou 515041, China
| | - Dong Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150000, China
| | - En-Min Li
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, China
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11
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Ruiz M, Ganfornina MD, Correnti C, Strong RK, Sanchez D. Ligand binding-dependent functions of the lipocalin NLaz: an in vivo study in Drosophila. FASEB J 2013; 28:1555-67. [PMID: 24361577 DOI: 10.1096/fj.13-240556] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Lipocalins are small extracellular proteins mostly described as lipid carriers. The Drosophila lipocalin NLaz (neural Lazarillo) modulates the IIS pathway and regulates longevity, stress resistance, and behavior. Here, we test whether a native hydrophobic pocket structure is required for NLaz to perform its functions. We use a point mutation altering the binding pocket (NLaz(L130R)) and control mutations outside NLaz binding pocket. Tryptophan fluorescence titration reveals that NLaz(L130R) loses its ability to bind ergosterol and the pheromone 7(z)-tricosene but retains retinoic acid binding. Using site-directed transgenesis in Drosophila, we test the functionality of the ligand binding-altered lipocalin at the organism level. NLaz-dependent life span reduction, oxidative stress and starvation sensitivity, aging markers accumulation, and deficient courtship are rescued by overexpression of NLaz(WT), but not of NLaz(L130R). Transcriptional responses to aging and oxidative stress show a large set of age-responsive genes dependent on the integrity of NLaz binding pocket. Inhibition of IIS activity and modulation of oxidative stress and infection-responsive genes are binding pocket-dependent processes. Control of energy metabolites on starvation appears to be, however, insensitive to the modification of the NLaz binding pocket.
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Affiliation(s)
- Mario Ruiz
- 2Instituto de Biología y Genética Molecular, c/Sanz y Forés 3, Universidad de Valladolid-CSIC, 47003 Valladolid, Spain.
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Abstract
Lipocalins are a family of diverse low molecular weight proteins that act extracellularly. They use multiple recognition properties that include 1) ligand binding to small hydrophobic molecules, 2) macromolecular complexation with other soluble macromolecules, and 3) binding to specific cell surface receptors to deliver cargo. Tear lipocalin (TLC) is a major protein in tears and has a large ligand-binding cavity that allows the lipocalin to bind an extensive and diverse set of lipophilic molecules. TLC can also bind to macromolecules, including the tear proteins lactoferin and lysozyme. The receptor to which TLC binds is termed tear lipocalin-interacting membrane receptor (LIMR). LIMR appears to work by endocytosis. TLC has a variety of suggested functions in tears, including regulation of tear viscosity, binding and release of lipids, endonuclease inactivation of viral DNA, binding of microbial siderophores (iron chelators used to deliver essential iron to bacteria), serving as a biomarker for dry eye, and possessing anti-inflammatory activity. Additional research is warranted to determine the actual functions of TLC in tears and the presence of its receptor on the ocular surface.
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Affiliation(s)
- Darlene A Dartt
- Schepens Eye Research Institute and Harvard Medical School, Boston, MA 02114, USA.
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13
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Albalat R, Brunet F, Laudet V, Schubert M. Evolution of retinoid and steroid signaling: vertebrate diversification from an amphioxus perspective. Genome Biol Evol 2011; 3:985-1005. [PMID: 21856648 PMCID: PMC3184775 DOI: 10.1093/gbe/evr084] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Although the physiological relevance of retinoids and steroids in vertebrates is very well established, the origin and evolution of the genetic machineries implicated in their metabolic pathways is still very poorly understood. We investigated the evolution of these genetic networks by conducting an exhaustive survey of components of the retinoid and steroid pathways in the genome of the invertebrate chordate amphioxus (Branchiostoma floridae). Due to its phylogenetic position at the base of chordates, amphioxus is a very useful model to identify and study chordate versus vertebrate innovations, both on a morphological and a genomic level. We have characterized more than 220 amphioxus genes evolutionarily related to vertebrate components of the retinoid and steroid pathways and found that, globally, amphioxus has orthologs of most of the vertebrate components of these two pathways, with some very important exceptions. For example, we failed to identify a vertebrate-like machinery for retinoid storage, transport, and delivery in amphioxus and were also unable to characterize components of the adrenal steroid pathway in this invertebrate chordate. The absence of these genes from the amphioxus genome suggests that both an elaboration and a refinement of the retinoid and steroid pathways took place at the base of the vertebrate lineage. In stark contrast, we also identified massive amplifications in some amphioxus gene families, most extensively in the short-chain dehydrogenase/reductase superfamily, which, based on phylogenetic and genomic linkage analyses, were likely the result of duplications specific to the amphioxus lineage. In sum, this detailed characterization of genes implicated in retinoid and steroid signaling in amphioxus allows us not only to reconstruct an outline of these pathways in the ancestral chordate but also to discuss functional innovations in retinoid homeostasis and steroid-dependent regulation in both cephalochordate and vertebrate evolution.
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Affiliation(s)
- Ricard Albalat
- Departament de Genètica, Facultat de Biologia and Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Spain.
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14
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Diversity of anti-haemostatic proteins in the salivary glands of Rhodnius species transmitters of Chagas disease in the greater Amazon. J Proteomics 2011; 74:1664-72. [DOI: 10.1016/j.jprot.2011.06.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Revised: 06/20/2011] [Accepted: 06/21/2011] [Indexed: 11/20/2022]
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15
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Peng Y, Liu J, Liu Q, Yao Y, Guo C, Zhang Y, Lin D. Conformational and biochemical characterization of a rat epididymis-specific lipocalin 12 expressed in Escherichia coli. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1804:2102-10. [DOI: 10.1016/j.bbapap.2010.07.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2010] [Revised: 06/14/2010] [Accepted: 07/23/2010] [Indexed: 12/31/2022]
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16
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An alpha-1-acid glycoprotein-like protein as a major component of the ovarian cavity fluid of viviparous fish, Neoditrema ransonnetii (Perciformes, Embiotocidae). Comp Biochem Physiol A Mol Integr Physiol 2009; 153:222-9. [PMID: 19245844 DOI: 10.1016/j.cbpa.2009.02.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2008] [Revised: 02/12/2009] [Accepted: 02/12/2009] [Indexed: 11/26/2022]
Abstract
Developing fetuses of surfperch (Neoditrema ransonnetii, Perciformes; Embiotocidae) are retained in the ovarian cavity until birth, where they are surrounded by ovarian cavity fluid (OCF). Expecting the OCF to have key roles in maintaining pregnancy, we purified and characterized a major glycoprotein of 51 kDa in the OCF of surfperch. On the basis of the N-terminal amino acid sequence, we cloned and sequenced a full-length cDNA. The deduced sequence comprises 214 amino acids (aa) including a signal peptide of 20 aa and a mature protein of 194 aa. This protein had an extremely low pI (below 2.8) and extraordinarily high glycosylation rate (more than 50%), characteristics being shared with alpha-1-acid glycoprotein (AGP), a member of the lipocalin superfamily. A homology search and phylogenetic analysis indicated that the 51 kDa protein and tributyltin-binding protein found in Japanese flounder are the closest known relatives of AGP. We therefore named the protein nrF-AGP. Messenger RNA of nrF-AGP was expressed intensively in the liver, but not at all in the ovarian tissue. Because nrF-AGP is the most salient component in OCF but not in plasma, we reasoned that it was selectively sequestered from blood to the ovarian cavity in pregnant females, and consequently, plays crucial roles in pregnancy.
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Machnes Z, Avtalion R, Shirak A, Trombka D, Wides R, Fellous M, Don J. Male-specific protein (MSP): a new gene linked to sexual behavior and aggressiveness of tilapia males. Horm Behav 2008; 54:442-9. [PMID: 18534590 DOI: 10.1016/j.yhbeh.2008.03.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2007] [Revised: 03/28/2008] [Accepted: 03/28/2008] [Indexed: 10/22/2022]
Abstract
MSP is a male-specific protein initially identified in the serum of sexually active Sarotherodon galilaeus males, and is shown herein to be present in the serum of sexually mature males, but not females, of three other tilapia species. Cloning of the MSP cDNA and analysis of its predicted amino-acid sequence revealed that it is an outlier lipocalin that contains a signal peptide in its N-terminal region. The abundance of highly homologous sequences found in fish and the monophyletic relationship to tetrapod Alpha-1-acid glycoprotein (AGP) places it as a clade XII lipocalin. MSP was shown to undergo major N-glycosylation, characteristic of many lipocalins. The expression pattern of MSP, as determined at both the RNA and protein levels, points to the liver, head kidney and testis as production tissues, and resembles a pattern typical of some hormones. We found that MSP is secreted in urine and seminal fluids, and is present in the skin mucus of socially dominant males. Moreover, we discovered a positive correlation between MSP levels in the serum and the dominance and aggressive behavior displayed by socially dominant males. Based on these data, we suggest that MSP is a novel male-specific lipocalin that may function in intra and inter-sex communication.
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Affiliation(s)
- Ziv Machnes
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 52900 Israel
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18
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Human ApoD, an apolipoprotein up-regulated in neurodegenerative diseases, extends lifespan and increases stress resistance in Drosophila. Proc Natl Acad Sci U S A 2008; 105:7088-93. [PMID: 18458334 DOI: 10.1073/pnas.0800896105] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Apolipoprotein D (ApoD) expression increases in several neurological disorders and in spinal cord injury. We provide a report of a physiological role for human ApoD (hApoD): Flies overexpressing hApoD are long-lived and protected against stress conditions associated with aging and neurodegeneration, including hyperoxia, dietary paraquat, and heat stress. We show that the fly ortholog, Glial Lazarillo, is strongly up-regulated in response to these extrinsic stresses and also can protect in vitro-cultured cells in situations modeling Alzheimer's disease (AD) and Parkinson's disease (PD). In adult flies, hApoD overexpression reduces age-associated lipid peroxide accumulation, suggesting a proximal mechanism of action. Similar data obtained in the mouse [Ganfornina, M.D., et al., (2008) Apolipoprotein D is involved in the mechanisms regulating protection from oxidative stress. Aging Cell 10.1111/j.1474-9726.2008.00395.] as well as in plants (Charron et al., personal communication) suggest that ApoD and its orthologs play an evolutionarily conserved role in response to stress, possibly managing or preventing lipid peroxidation.
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Reis C, Andrade S, Ramos O, Ramos C, Ho P, Batista I, Chudzinski-Tavassi A. Lopap, a prothrombin activator from Lonomia obliqua belonging to the lipocalin family: recombinant production, biochemical characterization and structure-function insights. Biochem J 2006; 398:295-302. [PMID: 16734589 PMCID: PMC1550302 DOI: 10.1042/bj20060325] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Using a cDNA library made from Lonomia obliqua caterpillar bristles, we identified a transcript with a 603 bp open reading frame. The deduced protein corresponds to Lopap, a prothrombin activator previously isolated by our group from the bristles of this species. The mature protein is composed by 185 amino acids and shares similarity with members of the lipocalin family. The cDNA encoding the mature form was amplified by PCR, subcloned into pAE vector and used to transform Escherichia coli BL21(DE3) cells. As for the native Lopap, the recombinant fusion protein shows enzymatic activity, promotes prothrombin hydrolysis, generates fragments similar to prethrombin-2 and fragment 1.2 as intermediates, and generates thrombin as the final product. In addition, structural bioinformatics studies indicated several interesting molecular features, including the residues that could be responsible for Lopap's serine protease-like activity and the role of calcium binding in this context. Such catalytic activity has never been found in other members of the lipocalin family. This is the first report describing the recombinant production and biochemical characterization of a Lonomia obliqua lipocalin, as well as the structural features that could be responsible for its serine protease-like catalytic activity.
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Affiliation(s)
- Cleyson Valença Reis
- *Laboratório de Bioquímica e Biofísica, Instituto Butantan, 1500 Av. Vital Brazil, CEP 05503-900, São Paulo, SP, Brazil
| | - Sonia Aparecida Andrade
- †Laboratório de Hemostasia, Instituto de Ensino e Pesquisa Hospital Sírio Libanês, 69 Rua Cel. Nicolau dos Santos, CEP 01308-050, São Paulo, SP, Brazil
| | - Oscar Henrique Pereira Ramos
- *Laboratório de Bioquímica e Biofísica, Instituto Butantan, 1500 Av. Vital Brazil, CEP 05503-900, São Paulo, SP, Brazil
| | - Celso Raul Romero Ramos
- ‡Centro de Biotecnologia, Instituto Butantan, 1500 Av. Vital Brazil, CEP 05503-900, São Paulo, SP, Brazil
| | - Paulo Lee Ho
- ‡Centro de Biotecnologia, Instituto Butantan, 1500 Av. Vital Brazil, CEP 05503-900, São Paulo, SP, Brazil
| | | | - Ana Marisa Chudzinski-Tavassi
- *Laboratório de Bioquímica e Biofísica, Instituto Butantan, 1500 Av. Vital Brazil, CEP 05503-900, São Paulo, SP, Brazil
- To whom correspondence should be addressed (email )
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20
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Grzyb J, Latowski D, Strzałka K. Lipocalins - a family portrait. JOURNAL OF PLANT PHYSIOLOGY 2006; 163:895-915. [PMID: 16504339 DOI: 10.1016/j.jplph.2005.12.007] [Citation(s) in RCA: 112] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2005] [Accepted: 12/12/2005] [Indexed: 05/06/2023]
Abstract
Lipocalins are a widely distributed group of proteins whose common feature is the presence of six-or eight-stranded beta-barrel in their tertiary structure and highly conservative motifs short conserved region, (SCR) in their amino acid sequences. The presence of three SCRs is typical for kernel lipocalins, while outlier lipocalins have only one or two such regions. Owing to their ability to bind and transport small, hydrophobic molecules, lipocalins participate in the distribution of such substances. However, the physiological significance of lipocalins is not limited to transfer processes. They play an important role in the regulation of immunological and developmental processes, and are also involved in the reactions of organisms to various stress factors and in the pathways of signal transduction. Of special interest is the enzymatic activity found in a few members of the lipocalin family, as well as the interaction with natural membranes, both directly with lipids and through membrane-localized protein receptors.
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Affiliation(s)
- Joanna Grzyb
- Department of Plant Physiology and Biochemistry, Faculty of Biotechnology, Jagiellonian University, Gronostajowa 7, Kraków, Poland
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21
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Campanacci V, Bishop RE, Blangy S, Tegoni M, Cambillau C. The membrane bound bacterial lipocalin Blc is a functional dimer with binding preference for lysophospholipids. FEBS Lett 2006; 580:4877-83. [PMID: 16920109 PMCID: PMC5007124 DOI: 10.1016/j.febslet.2006.07.086] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2006] [Revised: 07/26/2006] [Accepted: 07/28/2006] [Indexed: 11/16/2022]
Abstract
Lipocalins, a widespread multifunctional family of small proteins (15-25kDa) have been first described in eukaryotes and more recently in Gram-negative bacteria. Bacterial lipocalins belonging to class I are outer membrane lipoproteins, among which Blc from E. coli is the better studied. Blc is expressed under conditions of starvation and high osmolarity, conditions known to exert stress on the cell envelope. The structure of Blc that we have previously solved (V. Campanacci, D. Nurizzo, S. Spinelli, C. Valencia, M. Tegoni, C. Cambillau, FEBS Lett. 562 (2004) 183-188.) suggested its possible role in binding fatty acids or phospholipids. Both physiological and structural data on Blc, therefore, point to a role in storage or transport of lipids necessary for membrane maintenance. In order to further document this hypothesis for Blc function, we have performed binding studies using fluorescence quenching experiments. Our results indicate that dimeric Blc binds fatty acids and phospholipids in a micromolar K(d) range. The crystal structure of Blc with vaccenic acid, an unsaturated C18 fatty acid, reveals that the binding site spans across the Blc dimer, opposite to its membrane anchored face. An exposed unfilled pocket seemingly suited to bind a polar group attached to the fatty acid prompted us to investigate lyso-phospholipids, which were found to bind in a nanomolar K(d) range. We discuss these findings in terms of a potential role for Blc in the metabolism of lysophospholipids generated in the bacterial outer membrane.
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Affiliation(s)
- Valérie Campanacci
- Architecture et Fonction des Macromolecules Biologiques, UMR 6098, CNRS-Université s Aix-Marseille I & II, Campus de Luminy, Case 932, 163 Avenue de Luminy 13288 Marseille Cedex 09, France
| | - Russell E. Bishop
- Department of Biochemistry and Biomedical Sciences, McMaster University, Health Sciences Centre 4H19, 1200 Main Street West, Hamilton, Ont., Canada L8N 3Z5
| | - Stéphanie Blangy
- Architecture et Fonction des Macromolecules Biologiques, UMR 6098, CNRS-Université s Aix-Marseille I & II, Campus de Luminy, Case 932, 163 Avenue de Luminy 13288 Marseille Cedex 09, France
| | - Mariella Tegoni
- Architecture et Fonction des Macromolecules Biologiques, UMR 6098, CNRS-Université s Aix-Marseille I & II, Campus de Luminy, Case 932, 163 Avenue de Luminy 13288 Marseille Cedex 09, France
| | - Christian Cambillau
- Architecture et Fonction des Macromolecules Biologiques, UMR 6098, CNRS-Université s Aix-Marseille I & II, Campus de Luminy, Case 932, 163 Avenue de Luminy 13288 Marseille Cedex 09, France
- Corresponding author. Fax: +33 491 266 720. (C. Cambillau)
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22
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Walker DW, Muffat J, Rundel C, Benzer S. Overexpression of a Drosophila Homolog of Apolipoprotein D Leads to Increased Stress Resistance and Extended Lifespan. Curr Biol 2006; 16:674-9. [PMID: 16581512 DOI: 10.1016/j.cub.2006.01.057] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2005] [Revised: 01/25/2006] [Accepted: 01/26/2006] [Indexed: 11/21/2022]
Abstract
Increased Apolipoprotein D (ApoD) expression has been reported in various neurological disorders, including Alzheimer's disease, schizophrenia, and stroke, and in the aging brain . However, whether ApoD is toxic or a defense is unknown. In a screen to identify genes that protect Drosophila against acute oxidative stress, we isolated a fly homolog of ApoD, Glial Lazarillo (GLaz). In independent transgenic lines, overexpression of GLaz resulted in increased resistance to hyperoxia (100% O(2)) as well as a 29% extension of lifespan under normoxia. These flies also displayed marked improvements in climbing and walking ability after sublethal exposure to hyperoxia. Overexpression of Glaz also increased resistance to starvation without altering lipid or protein content. To determine whether GLaz might be important in protection against reperfusion injury, we subjected the flies to hypoxia, followed by recovery under normoxia. Overexpression of GLaz was protective against behavioral deficits caused in normal flies by this ischemia/reperfusion paradigm. This and the accompanying paper by Sanchez et al. (in this issue of Current Biology) are the first to manipulate the levels of an ApoD homolog in a model organism. Our data suggest that human ApoD may play a protective role and thus may constitute a therapeutic target to counteract certain neurological diseases.
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Affiliation(s)
- David W Walker
- Division of Biology, California Institute of Technology, Pasadena, 91125, USA
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Charron JBF, Ouellet F, Pelletier M, Danyluk J, Chauve C, Sarhan F. Identification, expression, and evolutionary analyses of plant lipocalins. PLANT PHYSIOLOGY 2005; 139:2017-28. [PMID: 16306142 PMCID: PMC1310578 DOI: 10.1104/pp.105.070466] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Lipocalins are a group of proteins that have been characterized in bacteria, invertebrate, and vertebrate animals. However, very little is known about plant lipocalins. We have previously reported the cloning of the first true plant lipocalins. Here we report the identification and characterization of plant lipocalins and lipocalin-like proteins using an integrated approach of data mining, expression studies, cellular localization, and phylogenetic analyses. Plant lipocalins can be classified into two groups, temperature-induced lipocalins (TILs) and chloroplastic lipocalins (CHLs). In addition, violaxanthin de-epoxidases (VDEs) and zeaxanthin epoxidases (ZEPs) can be classified as lipocalin-like proteins. CHLs, VDEs, and ZEPs possess transit peptides that target them to the chloroplast. On the other hand, TILs do not show any targeting peptide, but localization studies revealed that the proteins are found at the plasma membrane. Expression analyses by quantitative real-time PCR showed that expression of the wheat (Triticum aestivum) lipocalins and lipocalin-like proteins is associated with abiotic stress response and is correlated with the plant's capacity to develop freezing tolerance. In support of this correlation, data mining revealed that lipocalins are present in the desiccation-tolerant red algae Porphyra yezoensis and the cryotolerant marine yeast Debaryomyces hansenii, suggesting a possible association with stress-tolerant organisms. Considering the plant lipocalin properties, tissue specificity, response to temperature stress, and their association with chloroplasts and plasma membranes of green leaves, we hypothesize a protective function of the photosynthetic system against temperature stress. Phylogenetic analyses suggest that TIL lipocalin members in higher plants were probably inherited from a bacterial gene present in a primitive unicellular eukaryote. On the other hand, CHLs, VDEs, and ZEPs may have evolved from a cyanobacterial ancestral gene after the formation of the cyanobacterial endosymbiont from which the chloroplast originated.
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24
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Fan Y, Gore JC, Redding KO, Vailes LD, Chapman MD, Schal C. Tissue localization and regulation by juvenile hormone of human allergen Bla g 4 from the German cockroach, Blattella germanica (L.). INSECT MOLECULAR BIOLOGY 2005; 14:45-53. [PMID: 15663774 DOI: 10.1111/j.1365-2583.2004.00530.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The German cockroach, Blattella germanica (L.), produces several potent protein aeroallergens, including Bla g 4, a approximately 20 kDa lipocalin. RT-PCR, Northern analyses and in situ hybridization showed that Bla g 4 is expressed only in the adult male reproductive system. Western blotting and ELISA with rBla g 4 antiserum detected immunoreactivity in the utricles and the conglobate gland, but not in other tissues of the male reproductive system. The Bla g 4 protein content of males increased from adult emergence to day 14, but during copulation Bla g 4 was depleted in the male and transferred to the female within the spermatophore. Topical application of juvenile hormone III stimulated Bla g 4 production by both conglobate gland and utricles.
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Affiliation(s)
- Y Fan
- Department of Entomology and W. M. Keck Center for Behavioural Biology, North Carolina State University, Raleigh, NC 27695, USA
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25
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Pagano A, Giannoni P, Zambotti A, Sánchez D, Ganfornina MD, Gutiérrez G, Randazzo N, Cancedda R, Dozin B. Phylogeny and regulation of four lipocalin genes clustered in the chicken genome: evidence of a functional diversification after gene duplication. Gene 2004; 331:95-106. [PMID: 15094195 DOI: 10.1016/j.gene.2004.02.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2003] [Revised: 01/20/2004] [Accepted: 02/04/2004] [Indexed: 01/02/2023]
Abstract
A novel lipocalin gene is here reported that represents the fourth member of a cluster we have identified in the chicken genome. This cluster also includes Chondrogenesis-Associated Lipocalins beta and gamma (CAL beta, CAL gamma) and Extracellular Fatty Acid Binding Protein (Ex-FABP). The new gene codes for a 22-kDa secreted protein with three cysteine residues and a series of sequence features well conserved in the lipocalin family. All the genes in the cluster are structurally similar presenting comparable exon/intron boundary positions and exon sizes. A phylogenetic analysis indicates the monophyletic grouping of these genes, and their relationship with the lipocalins alpha-1-microglobulin (A1mg), complement factor 8 gamma chain (C8GC), prostaglandin D synthase (PGDS), and neutrophil-gelatinase-associated lipocalin (NGAL). The new cluster gene appears to be the ortholog of the mammalian C8GC and was thus named Ggal-C8GC. This orthology also suggests that this lipocalin was present in the ancestor common to reptiles and mammals. In addition to other expressing tissues, Ex-FABP, CAL beta and CAL gamma genes are highly transcribed in chondrocytes at late stages of chondrogenesis during endochondral bone formation and/or upon inflammatory stimulation. Here, we show that they are also transcriptionally induced when chondrocytes are subjected to various biological events as cell quiescence, cell shape transition, and hormonal stimulation. By contrast, Ggal-C8GC transcripts are only barely detectable in chondrocytes, but are more abundant in liver, kidney, brain, heart, skeletal muscle and particularly in skin. Moreover, no expression induction was observed neither during chondrocyte differentiation, nor upon any of the stimulations mentioned above. This indicates that the Ggal-C8GC gene was co-opted for a novel function after the duplication events that gave rise to the cluster. The peculiar coordinated regulation of Ex-FABP, CAL beta and CAL gamma, and the apparent divergent role of Ggal-C8GC suggest that these gene duplications may have been maintained during evolution by a sub-functionalization mechanism where some common function(s) are shared by several members of the cluster and some other specialized function(s) are unique to other members.
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Affiliation(s)
- Aldo Pagano
- Dipartimento di Oncologia, Biologia e Genetica, Università di Genova, 16132 Genoa, Italy
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Mans BJ, Neitz AWH. Exon-intron structure of outlier tick lipocalins indicate a monophyletic origin within the larger lipocalin family. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2004; 34:585-594. [PMID: 15147759 DOI: 10.1016/j.ibmb.2004.03.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2004] [Revised: 03/23/2004] [Accepted: 03/26/2004] [Indexed: 05/24/2023]
Abstract
All tick proteins assigned to the lipocalin family lack the structural conserved regions (SCRs) that are characteristic of the kernel lipocalins and can thus be classified as outliers. These tick proteins have been assigned to the tick lipocalin family based on database searches that indicated homology between tick sequences and the fact that the histamine binding protein (HBP2) from the hard tick Rhipicephalus appendiculatus (Ixodidae) shows structural similarity to the lipocalin fold. Sequence identity between kernel and outlier lipocalins falls below 20% and the question raised is whether the outlier and kernel lipocalins are truly homologous. More specifically in the case of the tick lipocalins, whether their structural fold is derived from the lipocalin fold or whether convergent evolution resulted in the generation of the basic lipocalin-like fold which consists of an eight stranded continuous anti-parallel beta-barrel terminated by a C-terminal alpha-helix that lies parallel to the barrel. The current study determined the gene structure for HBP2 and TSGP1, TSGP2 and TSGP4, lipocalins identified from the soft tick Ornithodoros savignyi (Argasidae). All tick lipocalins have four introns (A-D) with conserved positions and phases within the tick lipocalin sequence alignment. The positions and phase information are also conserved with regard to the rest of the lipocalin family. Phylogenetic analysis using this information shows conclusively that tick lipocalins are evolutionary related to the rest of the lipocalin family. Tick lipocalins are grouped within a monophyletic clade that indicates a monophyletic origin within the tick lineage and also group with the other arthropod lipocalins in a larger clade. Phylogenetic analysis of sequence alignments based on conserved secondary structure of the lipocalin fold support the conclusions from the gene structure trees. These results indicate that exon-intron arrangement can be useful for the inclusion of outlier lipocalins within the larger lipocalin family.
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Affiliation(s)
- Ben J Mans
- Department of Biochemistry, University of Pretoria, Pretoria 0002, South Africa.
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27
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Rzychon M, Filipek R, Sabat A, Kosowska K, Dubin A, Potempa J, Bochtler M. Staphostatins resemble lipocalins, not cystatins in fold. Protein Sci 2004; 12:2252-6. [PMID: 14500882 PMCID: PMC2366914 DOI: 10.1110/ps.03247703] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Staphostatins are the endogenous inhibitors of the major secreted cysteine proteases of Staphylococcus aureus, the staphopains. Here, we present the 1.4 A crystal structure of staphostatin B and show that the fold can be described as a fully closed, highly sheared eight-stranded beta-barrel. Thus, staphostatin B is related to beta-barrel domains that are involved in the inhibition or regulation of proteases of various catalytic types and to the superfamily of lipocalins/cytosolic fatty acid binding proteins. Unexpectedly for a cysteine protease inhibitor, staphostatin B is not significantly similar to cystatins.
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Affiliation(s)
- Malgorzata Rzychon
- International Institute of Molecular and Cell Biology, 02109 Warsaw, Poland
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28
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Campanacci V, Nurizzo D, Spinelli S, Valencia C, Tegoni M, Cambillau C. The crystal structure of the Escherichia coli lipocalin Blc suggests a possible role in phospholipid binding. FEBS Lett 2004; 562:183-8. [PMID: 15044022 DOI: 10.1016/s0014-5793(04)00199-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2004] [Revised: 02/19/2004] [Accepted: 02/19/2004] [Indexed: 10/26/2022]
Abstract
Lipocalins form a large multifunctional family of small proteins (15-25 kDa) first discovered in eukaryotes. More recently, several types of bacterial lipocalins have been reported, among which Blc from Escherichia coli is an outer membrane lipoprotein. As part of our structural genomics effort on proteins from E. coli, we have expressed, crystallized and solved the structure of Blc at 1.8 A resolution using remote SAD with xenon. The structure of Blc, the first of a bacterial lipocalin, exhibits a classical fold formed by a beta-barrel and a alpha-helix similar to that of the moth bilin binding protein. Its empty and open cavity, however, is too narrow to accommodate bilin, while the alkyl chains of two fatty acids or of a phospholipid could be readily modeled inside the cavity. Blc was reported to be expressed under stress conditions such as starvation or high osmolarity, during which the cell envelope suffers and requires maintenance. These data, together with our structural interpretation, suggest a role for Blc in storage or transport of lipids necessary for membrane repair or maintenance.
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Affiliation(s)
- Valérie Campanacci
- Architecture et Fonction des Macromolécules Biologiques, UMR 6098, CNRS and Universités Aix-Marseille I and II, 31 chemin J. Aiguier, F-13402 Marseille Cedex 20, France
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Sánchez D, Martínez S, Lindqvist A, Akerström B, Falkenberg C. Expression of the AMBP gene transcript and its two protein products, alpha(1)-microglobulin and bikunin, in mouse embryogenesis. Mech Dev 2002; 117:293-8. [PMID: 12204273 DOI: 10.1016/s0925-4773(02)00202-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The expression pattern of the alpha(1)-microglobulin/bikunin precursor (AMBP) gene, and its two protein products were studied in mouse embryos of 8.5-15.5 days of embryonic development by in situ hybridization and immunohistochemistry. AMBP mRNA is strongly transcribed in liver parenchyma, pancreas, and intestine epithelium. Sites of weaker expression are the vessels of the umbilical cord, the developing vertebral bodies, and kidney. The alpha(1)-microglobulin and bikunin proteins are accordingly present in developing hepatocytes, pancreas, kidney, and gut. However, additional sites of protein distribution were found that do not correlate to mRNA localization: alpha(1)-microglobulin was found in myocytes and bikunin in cardiac muscle, nervous system microvasculature, and connective tissue. Both proteins were found in brain mesenchyme and meninges. Thus, a restricted expression of the AMBP mRNA in a few organs contrasts to a widespread and unique distribution of each of the two proteins.
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Affiliation(s)
- Diego Sánchez
- Instituto de Neurociencias, Universidad Miguel Hernández-CSIC, Alicante, Spain.
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Seppälä M, Taylor RN, Koistinen H, Koistinen R, Milgrom E. Glycodelin: a major lipocalin protein of the reproductive axis with diverse actions in cell recognition and differentiation. Endocr Rev 2002; 23:401-30. [PMID: 12202458 DOI: 10.1210/er.2001-0026] [Citation(s) in RCA: 178] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Glycodelin is a glycoprotein that belongs to the lipocalin superfamily. Depending on glycosylation, glycodelin appears in various isoforms. In the uterus, glycodelin-A is the major progesterone-regulated glycoprotein secreted into uterine luminal cavity by secretory/decidualized endometrial glands. The other tissues expressing glycodelin include fallopian tubes, ovary, breast, seminal vesicle, bone marrow, and eccrine glands. Glycodelin-A potently and dose-dependently inhibits human sperm-egg binding, whereas differently glycosylated glycodelin-S from seminal plasma has no such effect. Absence of contraceptive glycodelin-A in the uterus during periovulatory midcycle is consistent with an open "fertile window." Glycodelin induced by local or systemic administration of progestogens may potentially reduce the fertilizing capacity of sperm in any phase of the menstrual cycle. Glycodelin also has immunosuppressive activity. Its high concentration at the fetomaternal interface may contribute to protection of the embryonic semiallograft. Besides being an epithelial differentiation marker, glycodelin appears to play a role in glandular morphogenesis, as transfection of glycodelin cDNA into a glycodelin-negative breast cancer cells resulted in formation of gland-like structures, restricted proliferation, and induction of other epithelial markers. These various properties, as well as the chemistry, biology, and clinical aspects of glycodelin, continue to be areas of active investigation reviewed in this communication.
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Affiliation(s)
- Markku Seppälä
- Department of Obstetrics and Gynecology, Helsinki University Central Hospital, Haartmaninkatu 2, 00029 HUS, Helsinki, Finland.
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Fogolari F, Tessari S, Molinari H. Singular value decomposition analysis of protein sequence alignment score data. Proteins 2002; 46:161-70. [PMID: 11807944 DOI: 10.1002/prot.10032] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
One of the standard tools for the analysis of data arranged in matrix form is singular value decomposition (SVD). Few applications to genomic data have been reported to date mainly for the analysis of gene expression microarray data. We review SVD properties, examine mathematical terms and assumptions implicit in the SVD formalism, and show that SVD can be applied to the analysis of matrices representing pairwise alignment scores between large sets of protein sequences. In particular, we illustrate SVD capabilities for data dimension reduction and for clustering protein sequences. A comparison is performed between SVD-generated clusters of proteins and annotation reported in the SWISS-PROT Database for a set of protein sequences forming the calycin superfamily, entailing all entries corresponding to the lipocalin, cytosolic fatty acid-binding protein, and avidin-streptavidin Prosite patterns.
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Affiliation(s)
- F Fogolari
- Dipartimento Scientifico Tecnologico, Facoltà di Scienze, Università di Verona, Verona, Italy.
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32
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Sánchez D, Ganfornina MD, Martínez S. Expression pattern of the lipocalin apolipoprotein D during mouse embryogenesis. Mech Dev 2002; 110:225-9. [PMID: 11744388 DOI: 10.1016/s0925-4773(01)00578-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Apolipoprotein D (ApoD) is a secreted protein that belongs to the lipocalin family. We describe the expression pattern of ApoD during mouse embryogenesis by in situ hybridization using RNA probes. ApoD is expressed at E9 in mesenchymal cells in the rombencephalic-mesencephalic region. At E9.5 the cephalic ApoD-positive cells appear in the mesenchyme, and at later stages (starting at E10.5) ApoD expression is seen in meninges. Within the neuroepithelium, ApoD is expressed in pericytes surrounding brain and spinal cord capillaries from E10.5 to birth. Other places of expression of ApoD are the mesenchyme surrounding the olfactory epithelium and semicircular canals, as well as chondroblasts of skull and vertebrae.
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Affiliation(s)
- Diego Sánchez
- Instituto de Neurociencias de Alicante, Universidad Miguel Hernandez-CSIC, E-03550 Alicante, Spain.
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Cornette R, Farine JP, Quennedey B, Brossut R. Molecular characterization of a new adult male putative calycin specific to tergal aphrodisiac secretion in the cockroach Leucophaea maderae. FEBS Lett 2001; 507:313-7. [PMID: 11696362 DOI: 10.1016/s0014-5793(01)02997-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Lma-p18 is an epicuticular surface protein specific to the tergal gland aphrodisiac secretion of Leucophaea maderae adult males. Native Lma-p18 was purified and the complete cDNA sequence was determined by RT-PCR using primers based on Edman degradation fragments. Northern blot and in situ hybridization analyses showed that Lma-p18 is expressed exclusively in the anterior part of male tergal gland, which is exposed only during sexual behavior. Sequence analysis indicated that Lma-p18 belongs to the calycin superfamily and is very similar to Lma-p22, the first known male-specific tergal protein in L. maderae. Lma-p18 and Lma-p22 were proposed to bind different sexually attractive compounds as other calycins.
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Affiliation(s)
- R Cornette
- Développement-Communication chimique, Unité Mixte de Recherche 5548 du Centre National de la Recherche Scientifique, Université de Bourgogne, 6 Bd Gabriel, 21 000, Dijon, France
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Flower DR, North AC, Sansom CE. The lipocalin protein family: structural and sequence overview. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1482:9-24. [PMID: 11058743 DOI: 10.1016/s0167-4838(00)00148-5] [Citation(s) in RCA: 600] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Lipocalins are remarkably diverse at the sequence level yet have highly conserved structures. Most lipocalins share three characteristic conserved sequence motifs - the kernel lipocalins - while others are more divergent family members - the outlier lipocalins - typically sharing only one or two. This classification is a useful tool for analysing the family, and within these large sets are smaller groups sharing much higher levels of sequence similarity. The lipocalins are also part of a larger protein superfamily: the calycins, which includes the fatty acid binding proteins, avidins, a group of metalloproteinase inhibitors, and triabin. The superfamily is characterised by a similar structure (a repeated +1 topology beta-barrel) and by the conservation of a remarkable structural signature.
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Affiliation(s)
- D R Flower
- The Edward Jenner Institute for Vaccine Research, Newbury, Berkshire, UK.
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