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Rehman S, Aziz E, Akhtar W, Ilyas M, Mahmood T. Structural and functional characteristics of plant proteinase inhibitor-II (PI-II) family. Biotechnol Lett 2017; 39:647-666. [PMID: 28185031 DOI: 10.1007/s10529-017-2298-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 02/02/2017] [Indexed: 10/20/2022]
Abstract
Plant proteinase inhibitor-II (PI-II) proteins are one of the promising defensive proteins that helped the plants to resist against different kinds of unfavorable conditions. Different roles for PI-II have been suggested such as regulation of endogenous proteases, modulation of plant growth and developmental processes and mediating stress responses. The basic knowledge on genetic and molecular diversity of these proteins has provided significant insight into their gene structure and evolutionary relationships in various members of this family. Phylogenetic comparisons of these family genes in different plants suggested that the high rate of retention of gene duplication and inhibitory domain multiplication may have resulted in the expansion and functional diversification of these proteins. Currently, a large number of transgenic plants expressing PI-II genes are being developed for enhancing the defensive capabilities against insects, bacteria and pathogenic fungi. Much emphasis is yet to be given to exploit this ever expanding repertoire of genes for improving abiotic stress resistance in transgenic crops. This review presents an overview about the current knowledge on PI-II family genes, their multifunctional role in plant defense and physiology with their potential applications in biotechnology.
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Affiliation(s)
- Shazia Rehman
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Ejaz Aziz
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Wasim Akhtar
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Muhammad Ilyas
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Tariq Mahmood
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
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Vorster J, Rasoolizadeh A, Goulet MC, Cloutier C, Sainsbury F, Michaud D. Positive selection of digestive Cys proteases in herbivorous Coleoptera. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2015; 65:10-19. [PMID: 26264818 DOI: 10.1016/j.ibmb.2015.07.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 07/22/2015] [Accepted: 07/31/2015] [Indexed: 06/04/2023]
Abstract
Positive selection is thought to contribute to the functional diversification of insect-inducible protease inhibitors in plants in response to selective pressures exerted by the digestive proteases of their herbivorous enemies. Here we assessed whether a reciprocal evolutionary process takes place on the insect side, and whether ingestion of a positively selected plant inhibitor may translate into a measurable rebalancing of midgut proteases in vivo. Midgut Cys proteases of herbivorous Coleoptera, including the major pest Colorado potato beetle (Leptinotarsa decemlineata), were first compared using a codon-based evolutionary model to look for the occurrence of hypervariable, positively selected amino acid sites among the tested sequences. Hypervariable sites were found, distributed within -or close to- amino acid regions interacting with Cys-type inhibitors of the plant cystatin protein family. A close examination of L. decemlineata sequences indicated a link between their assignment to protease functional families and amino acid identity at positively selected sites. A function-diversifying role for positive selection was further suggested empirically by in vitro protease assays and a shotgun proteomic analysis of L. decemlineata Cys proteases showing a differential rebalancing of protease functional family complements in larvae fed single variants of a model cystatin mutated at positively selected amino acid sites. These data confirm overall the occurrence of hypervariable, positively selected amino acid sites in herbivorous Coleoptera digestive Cys proteases. They also support the idea of an adaptive role for positive selection, useful to generate functionally diverse proteases in insect herbivores ingesting functionally diverse, rapidly evolving dietary cystatins.
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Affiliation(s)
- Juan Vorster
- Département de phytologie, CRIV-Biotechnologie, Université Laval, Québec, QC G1V 0A6, Canada; Department of Plant and Soil Science, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Asieh Rasoolizadeh
- Département de phytologie, CRIV-Biotechnologie, Université Laval, Québec, QC G1V 0A6, Canada
| | - Marie-Claire Goulet
- Département de phytologie, CRIV-Biotechnologie, Université Laval, Québec, QC G1V 0A6, Canada
| | - Conrad Cloutier
- Département de biologie, Université Laval, Québec, QC G1V 0A6, Canada
| | - Frank Sainsbury
- Département de phytologie, CRIV-Biotechnologie, Université Laval, Québec, QC G1V 0A6, Canada; The University of Queensland, Australian Institute for Bioengineering and Nanotechnology, Centre for Biomolecular Engineering, St. Lucia, Queensland 4072, Australia
| | - Dominique Michaud
- Département de phytologie, CRIV-Biotechnologie, Université Laval, Québec, QC G1V 0A6, Canada.
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Neves F, Abrantes J, Almeida T, de Matos AL, Costa PP, Esteves PJ. Genetic characterization of interleukins (IL-1α, IL-1β, IL-2, IL-4, IL-8, IL-10, IL-12A, IL-12B, IL-15 and IL-18) with relevant biological roles in lagomorphs. Innate Immun 2015; 21:787-801. [PMID: 26395994 PMCID: PMC4609935 DOI: 10.1177/1753425915606209] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 08/17/2015] [Indexed: 12/11/2022] Open
Abstract
ILs, as essential innate immune modulators, are involved in an array of biological processes. In the European rabbit (Oryctolagus cuniculus) IL-1α, IL-1β, IL-2, IL-4, IL-8, IL-10, IL-12A, IL-12B, IL-15 and IL-18 have been implicated in inflammatory processes and in the immune response against rabbit hemorrhagic disease virus and myxoma virus infections. In this study we characterized these ILs in six Lagomorpha species (European rabbit, pygmy rabbit, two cottontail rabbit species, European brown hare and American pika). Overall, these ILs are conserved between lagomorphs, including in their exon/intron structure. Most differences were observed between leporids and American pika. Indeed, when comparing both, some relevant differences were observed in American pika, such as the location of the stop codon in IL-1α and IL-2, the existence of a different transcript in IL8 and the number of cysteine residues in IL-1β. Changes at N-glycosylation motifs were also detected in IL-1, IL-10, IL-12B and IL-15. IL-1α is the protein that presents the highest evolutionary distances, which is in contrast to IL-12A where the distances between lagomorphs are the lowest. For all these ILs, sequences of human and European rabbit are more closely related than between human and mouse or European rabbit and mouse.
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Affiliation(s)
- Fabiana Neves
- CIBIO, InBIO-Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Vairão, Portugal UMIB/UP-Unidade Multidisciplinar de Investigação Biomédica/Universidade do Porto, Porto, Portugal
| | - Joana Abrantes
- CIBIO, InBIO-Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Vairão, Portugal
| | - Tereza Almeida
- CIBIO, InBIO-Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Vairão, Portugal
| | - Ana Lemos de Matos
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Paulo P Costa
- UMIB/UP-Unidade Multidisciplinar de Investigação Biomédica/Universidade do Porto, Porto, Portugal Departmento Genética, CSPGF, Instituto Nacional de Saúde Dr. Ricardo Jorge, Porto, Portugal
| | - Pedro J Esteves
- CIBIO, InBIO-Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Vairão, Portugal Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal CITS-Centro de Investigação em Tecnologias de Saúde, CESPU, Gandra, Portugal
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Li XQ, Du D. Motif types, motif locations and base composition patterns around the RNA polyadenylation site in microorganisms, plants and animals. BMC Evol Biol 2014; 14:162. [PMID: 25052519 PMCID: PMC4360255 DOI: 10.1186/s12862-014-0162-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 07/14/2014] [Indexed: 12/22/2022] Open
Abstract
Background The polyadenylation of RNA is critical for gene functioning, but the conserved sequence motifs (often called signal or signature motifs), motif locations and abundances, and base composition patterns around mRNA polyadenylation [poly(A)] sites are still uncharacterized in most species. The evolutionary tendency for poly(A) site selection is still largely unknown. Results We analyzed the poly(A) site regions of 31 species or phyla. Different groups of species showed different poly(A) signal motifs: UUACUU at the poly(A) site in the parasite Trypanosoma cruzi; UGUAAC (approximately 13 bases upstream of the site) in the alga Chlamydomonas reinhardtii; UGUUUG (or UGUUUGUU) at mainly the fourth base downstream of the poly(A) site in the parasite Blastocystis hominis; and AAUAAA at approximately 16 bases and approximately 19 bases upstream of the poly(A) site in animals and plants, respectively. Polyadenylation signal motifs are usually several hundred times more abundant around poly(A) sites than in whole genomes. These predominant motifs usually had very specific locations, whether upstream of, at, or downstream of poly(A) sites, depending on the species or phylum. The poly(A) site was usually an adenosine (A) in all analyzed species except for B. hominis, and there was weak A predominance in C. reinhardtii. Fungi, animals, plants, and the protist Phytophthora infestans shared a general base abundance pattern (or base composition pattern) of “U-rich—A-rich—U-rich—Poly(A) site—U-rich regions”, or U-A-U-A-U for short, with some variation for each kingdom or subkingdom. Conclusion This study identified the poly(A) signal motifs, motif locations, and base composition patterns around mRNA poly(A) sites in protists, fungi, plants, and animals and provided insight into poly(A) site evolution.
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Affiliation(s)
- Xiu-Qing Li
- Molecular Genetics Laboratory, Potato Research Centre, Agriculture and Agri-Food Canada, 850 Lincoln Road, Fredericton, New Brunswick, E3B 4Z7, Canada.
| | - Donglei Du
- Quantitative Methods Research Group, Faculty of Business Administration, University of New Brunswick, 7 Macaulay Lane, Fredericton, NB, E3B 5A3, Canada.
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Convergent evolution of IL-6 in two leporids (Oryctolagus and Pentalagus) originated an extended protein. Immunogenetics 2014; 66:589-95. [DOI: 10.1007/s00251-014-0787-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 06/26/2014] [Indexed: 10/25/2022]
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Complementation of intramolecular interactions for structural-functional stability of plant serine proteinase inhibitors. Biochim Biophys Acta Gen Subj 2013; 1830:5087-94. [PMID: 23891708 DOI: 10.1016/j.bbagen.2013.07.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Revised: 07/15/2013] [Accepted: 07/18/2013] [Indexed: 11/20/2022]
Abstract
BACKGROUND Plant protease inhibitors (PIs) constitute a diverse group of proteins capable of inhibiting proteases. Among PIs, serine PIs (SPIs) display stability and conformational restrictions of the reactive site loop by virtue of their compact size, and by the presence of disulfide bonds, hydrogen bonds, and other weak interactions. SCOPE OF REVIEW The significance of various intramolecular interactions contributing to protein folding mechanism and their role in overall stability and activity of SPIs is discussed here. Furthermore, we have reviewed the effect of variation or manipulation of these interactions on the activity/stability of SPIs. MAJOR CONCLUSIONS The selective gain or loss of disulfide bond(s) in SPIs can be associated with their functional differentiation, which is likely to be compensated by non-covalent interactions (hydrogen bonding or electrostatic interactions). Thus, these intramolecular interactions are collectively responsible for the functional activity of SPIs, through the maintenance of scaffold framework, conformational rigidity and shape complementarities of reactive site loop. GENERAL SIGNIFICANCE Structural insight of these interactions will provide an in-depth understanding of kinetic and thermodynamic parameters involved in the folding and stability mechanisms of SPIs. These features can be explored for engineering canonical SPIs for optimizing their overall stability and functionality for various applications.
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Neves F, Abrantes J, Steinke JW, Esteves PJ. Maximum-likelihood approaches reveal signatures of positive selection in IL genes in mammals. Innate Immun 2013; 20:184-91. [PMID: 23775092 DOI: 10.1177/1753425913486687] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
ILs are part of the immune system and are involved in multiple biological activities. ILs have been shown to evolve under positive selection; however, little information exists regarding which codons are specifically selected. By using different codon-based maximum-likelihood (ML) approaches, signatures of positive selection in mammalian ILs were searched for. Sequences of 46 ILs were retrieved from publicly available databases of mammalian genomes to detect signatures of positive selection in individual codons. Evolutionary analyses were conducted under two ML frameworks, the HyPhy package implemented in the Data Monkey Web Server and CODEML implemented in PAML. Signatures of positive selection were found in 28 ILs: IL-1A and B; IL-2, IL-4 to IL-10, IL-12A and B; IL-14 to IL-17A and C; IL-18, IL-20 to IL-22, IL-25, IL-26, IL-27B, IL-31, IL-34, IL-36A; and G. Codons under positive selection varied between 1 and 15. No evidence of positive selection was detected in IL-13; IL-17B and F; IL-19, IL-23, IL-24, IL-27A; or IL-29. Most mammalian ILs have sites evolving under positive selection, which may be explained by the multitude of biological processes in which ILs are enrolled. The results obtained raise hypotheses concerning the ILs functions, which should be pursued by using mutagenesis and crystallographic approaches.
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Affiliation(s)
- Fabiana Neves
- 1CIBIO/UP - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Porto, Portugal
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Chakraborty C, George Priya Doss C, Bandyopadhyay S, Sarkar BK, Syed Haneef SA. Mapping the Structural Topology of IRS Family Cascades Through Computational Biology. Cell Biochem Biophys 2013; 67:1319-31. [DOI: 10.1007/s12013-013-9664-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Shen Y, Zeng L, Zhu A, Blanc T, Patel D, Pennello A, Bari A, Ng S, Persaud K, Kang YK, Balderes P, Surguladze D, Hindi S, Zhou Q, Ludwig DL, Snavely M. Removal of a C-terminal serine residue proximal to the inter-chain disulfide bond of a human IgG1 lambda light chain mediates enhanced antibody stability and antibody dependent cell-mediated cytotoxicity. MAbs 2013; 5:418-31. [PMID: 23567210 PMCID: PMC4169035 DOI: 10.4161/mabs.24291] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Optimization of biophysical properties is a critical success factor for the developability of monoclonal antibodies with potential therapeutic applications. The inter-domain disulfide bond between light chain (Lc) and heavy chain (Hc) in human IgG1 lends structural support for antibody scaffold stability, optimal antigen binding, and normal Fc function. Recently, human IgG1λ has been suggested to exhibit significantly greater susceptibility to reduction of the inter Lc-Hc disulfide bond relative to the same disulfide bond in human IgG1κ. To understand the molecular basis for this observed difference in stability, the sequence and structure of human IgG1λ and human IgG1κ were compared. Based on this Lc comparison, three single mutations were made in the λ Lc proximal to the cysteine residue, which forms a disulfide bond with the Hc. We determined that deletion of S214 (dS) improved resistance of the association between Lc and Hc to thermal stress. In addition, deletion of this terminal serine from the Lc of IgG1λ provided further benefit, including an increase in stability at elevated pH, increased yield from transient transfection, and improved in vitro antibody dependent cell-mediated cytotoxicity (ADCC). These observations support the conclusion that the presence of the terminal serine of the λ Lc creates a weaker inter-chain disulfide bond between the Lc and Hc, leading to slightly reduced stability and a potential compromise in IgG1λ function. Our data from a human IgG1λ provide a basis for further investigation of the effects of deleting terminal serine from λLc on the stability and function of other human IgG1λ antibodies.
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Affiliation(s)
- Yang Shen
- Department of Antibody Technology; ImClone Systems, a wholly-owned subsidiary of Eli Lilly and Company; New York, NY USA
| | - Lin Zeng
- Department of Antibody Technology; ImClone Systems, a wholly-owned subsidiary of Eli Lilly and Company; New York, NY USA
| | - Aiping Zhu
- Department of Antibody Technology; ImClone Systems, a wholly-owned subsidiary of Eli Lilly and Company; New York, NY USA
| | - Tim Blanc
- Department of Bioanalytical Sciences; ImClone Systems, a wholly-owned subsidiary of Eli Lilly and Company; Branchburg, NJ USA
| | - Dipa Patel
- Department of Immunology; ImClone Systems, a wholly-owned subsidiary of Eli Lilly and Company; New York, NY USA
| | - Anthony Pennello
- Department of Oncology Translational Medicine; ImClone Systems, a wholly-owned subsidiary of Eli Lilly and Company; New York, NY USA
| | - Amtul Bari
- Department of BioProcess Sciences; ImClone Systems, a wholly-owned subsidiary of Eli Lilly and Company; New York, NY USA
| | - Stanley Ng
- Department of BioProcess Sciences; ImClone Systems, a wholly-owned subsidiary of Eli Lilly and Company; New York, NY USA
| | - Kris Persaud
- Department of BioProcess Sciences; ImClone Systems, a wholly-owned subsidiary of Eli Lilly and Company; New York, NY USA
| | - Yun Kenneth Kang
- Department of BioProcess Sciences; ImClone Systems, a wholly-owned subsidiary of Eli Lilly and Company; New York, NY USA
| | - Paul Balderes
- Department of BioProcess Sciences; ImClone Systems, a wholly-owned subsidiary of Eli Lilly and Company; New York, NY USA
| | - David Surguladze
- Department of Oncology Translational Medicine; ImClone Systems, a wholly-owned subsidiary of Eli Lilly and Company; New York, NY USA
| | - Sagit Hindi
- Department of BioProcess Sciences; ImClone Systems, a wholly-owned subsidiary of Eli Lilly and Company; New York, NY USA
| | - Qinwei Zhou
- Department of Bioanalytical Sciences; ImClone Systems, a wholly-owned subsidiary of Eli Lilly and Company; Branchburg, NJ USA
| | - Dale L Ludwig
- Department of BioProcess Sciences; ImClone Systems, a wholly-owned subsidiary of Eli Lilly and Company; New York, NY USA
| | - Marshall Snavely
- Department of Antibody Technology; ImClone Systems, a wholly-owned subsidiary of Eli Lilly and Company; New York, NY USA
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Joshi RS, Mishra M, Tamhane VA, Ghosh A, Sonavane U, Suresh CG, Joshi R, Gupta VS, Giri AP. The remarkable efficiency of a Pin-II proteinase inhibitor sans two conserved disulfide bonds is due to enhanced flexibility and hydrogen bond density in the reactive site loop. J Biomol Struct Dyn 2012; 32:13-26. [PMID: 23256852 DOI: 10.1080/07391102.2012.745378] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Capsicum annuum (L.) expresses diverse potato type II family proteinase inhibitors comprising of inhibitory repeat domain (IRD) as basic functional unit. Most IRDs contain eight conserved cysteines forming four disulfide bonds, which are indispensible for their stability and activity. We investigated the functional significance of evolutionary variations in IRDs and their role in mediating interaction between the inhibitor and cognate proteinase. Among the 18 IRDs encoded by C. annuum, IRD-7, -9, and -12 were selected for further characterization on the basis of variation in their reactive site loop, number of conserved cysteine residues, and higher theoretical ΔGbind for interaction with Helicoverpa armigera trypsin. Moreover, inhibition kinetics showed that IRD-9, despite loss of some of the disulfide bonds, was a more potent proteinase inhibitor among the three selected IRDs. Molecular dynamic simulations revealed that serine residues in the place of cysteines at seventh and eighth positions of IRD-9 resulted in an increase in the density of intramolecular hydrogen bonds and reactive site loop flexibility. Results of the serine residues chemical modification also supported this observation and provided a possible explanation for the remarkable inhibitory potential of IRD-9. Furthermore, this natural variant among IRDs showed special attributes like stability to proteolysis and synergistic inhibitory effect on other IRDs. It is likely that IRDs have coevolved selective specialization of their structure and function as a response towards specific insect proteases they encountered. Understanding the molecular mechanism of pest protease-plant proteinaceous inhibitor interaction will help in developing effective pest control strategies. An animated interactive 3D complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:39.
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Affiliation(s)
- Rakesh S Joshi
- a Plant Molecular Biology Unit, Biochemical Sciences Division , CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune , 411 008 , MS , India
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Mishra M, Mahajan N, Tamhane VA, Kulkarni MJ, Baldwin IT, Gupta VS, Giri AP. Stress inducible proteinase inhibitor diversity in Capsicum annuum. BMC PLANT BIOLOGY 2012; 12:217. [PMID: 23153298 PMCID: PMC3511207 DOI: 10.1186/1471-2229-12-217] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Accepted: 11/07/2012] [Indexed: 05/02/2023]
Abstract
BACKGROUND Wound-inducible Pin-II Proteinase inhibitors (PIs) are one of the important plant serine PIs which have been studied extensively for their structural and functional diversity and relevance in plant defense against insect pests. To explore the functional specialization of an array of Capsicum annuum (L.) proteinase inhibitor (CanPIs) genes, we studied their expression, processing and tissue-specific distribution under steady-state and induced conditions. Inductions were performed by subjecting C. annuum leaves to various treatments, namely aphid infestation or mechanical wounding followed by treatment with either oral secretion (OS) of Helicoverpa armigera or water. RESULTS The elicitation treatments regulated the accumulation of CanPIs corresponding to 4-, 3-, and 2-inhibitory repeat domains (IRDs). Fourty seven different CanPI genes composed of 28 unique IRDs were identified in total along with those reported earlier. The CanPI gene pool either from uninduced or induced leaves was dominated by 3-IRD PIs and trypsin inhibitory domains. Also a major contribution by 4-IRD CanPI genes possessing trypsin and chymotrypsin inhibitor domains was specifically revealed in wounded leaves treated with OS. Wounding displayed the highest number of unique CanPIs while wounding with OS treatment resulted in the high accumulation of specifically CanPI-4, -7 and -10. Characterization of the PI protein activity through two dimensional gel electrophoresis revealed tissue and induction specific patterns. Consistent with transcript abundance, wound plus OS or water treated C. annuum leaves exhibited significantly higher PI activity and isoform diversity contributed by 3- and 4-IRD CanPIs. CanPI accumulation and activity was weakly elicited by aphid infestation yet resulted in the higher expression of CanPI-26, -41 and -43. CONCLUSIONS Plants can differentially perceive various kinds of insect attacks and respond appropriately through activating plant defenses including regulation of PIs at transcriptional and post-translational levels. Based on the differentially elicited CanPI accumulation patterns, it is intriguing to speculate that generating sequence diversity in the form of multi-IRD PIs is a part of elaborative plant defense strategy to obtain a diverse pool of functional units to confine insect attack.
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Affiliation(s)
- Manasi Mishra
- Plant Molecular Biology Unit, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, MS, 411 008, India
| | - Neha Mahajan
- Plant Molecular Biology Unit, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, MS, 411 008, India
| | - Vaijayanti A Tamhane
- Plant Molecular Biology Unit, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, MS, 411 008, India
- Present address: Institute of Bioinformatics and Biotechnology, University of Pune, Pune, MS, 411 007, India
| | - Mahesh J Kulkarni
- Plant Molecular Biology Unit, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, MS, 411 008, India
| | - Ian T Baldwin
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
| | - Vidya S Gupta
- Plant Molecular Biology Unit, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, MS, 411 008, India
| | - Ashok P Giri
- Plant Molecular Biology Unit, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, MS, 411 008, India
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Du D, Lee CF, Li XQ. Systematic differences in signal emitting and receiving revealed by PageRank analysis of a human protein interactome. PLoS One 2012; 7:e44872. [PMID: 23028653 PMCID: PMC3446998 DOI: 10.1371/journal.pone.0044872] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 08/08/2012] [Indexed: 11/18/2022] Open
Abstract
Most protein PageRank studies do not use signal flow direction information in protein interactions because this information was not readily available in large protein databases until recently. Therefore, four questions have yet to be answered: A) What is the general difference between signal emitting and receiving in a protein interactome? B) Which proteins are among the top ranked in directional ranking? C) Are high ranked proteins more evolutionarily conserved than low ranked ones? D) Do proteins with similar ranking tend to have similar subcellular locations? In this study, we address these questions using the forward, reverse, and non-directional PageRank approaches to rank an information-directional network of human proteins and study their evolutionary conservation. The forward ranking gives credit to information receivers, reverse ranking to information emitters, and non-directional ranking mainly to the number of interactions. The protein lists generated by the forward and non-directional rankings are highly correlated, but those by the reverse and non-directional rankings are not. The results suggest that the signal emitting/receiving system is characterized by key-emittings and relatively even receivings in the human protein interactome. Signaling pathway proteins are frequent in top ranked ones. Eight proteins are both informational top emitters and top receivers. Top ranked proteins, except a few species-related novel-function ones, are evolutionarily well conserved. Protein-subunit ranking position reflects subunit function. These results demonstrate the usefulness of different PageRank approaches in characterizing protein networks and provide insights to protein interaction in the cell.
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Affiliation(s)
- Donglei Du
- Quantiative Study Group, Faculty of Business Administration, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Connie F. Lee
- Quantiative Study Group, Faculty of Business Administration, University of New Brunswick, Fredericton, New Brunswick, Canada
- The Fu Foundation School of Engineering and Applied Science, Columbia University, New York, New York, United States of America
| | - Xiu-Qing Li
- Molecular Genetics Laboratory, Potato Research Centre, Agriculture and Agri-Food Canada, Fredericton, New Brunswick, Canada
- * E-mail:
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