1
|
Ganguly D. Multi-omics studies in interpreting the evolving standard model for immune functions. Brief Funct Genomics 2024; 23:75-81. [PMID: 36905355 DOI: 10.1093/bfgp/elad003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 01/11/2023] [Accepted: 01/23/2023] [Indexed: 03/12/2023] Open
Abstract
A standard model that is able to generalize data on myriad involvement of the immune system in organismal physio-pathology and to provide a unified evolutionary teleology for immune functions in multicellular organisms remains elusive. A number of such 'general theories of immunity' have been proposed based on contemporaneously available data, starting with the usual description of self-nonself discrimination, followed by the 'danger model' and the more recent 'discontinuity theory.' More recent data deluge on involvement of immune mechanisms in a wide variety of clinical contexts, a number of which fail to get readily accommodated into the available teleologic standard models, makes deriving a standard model of immunity more challenging. But technological advances enabling multi-omics investigations into an ongoing immune response, covering genome, epigenome, coding and regulatory transcriptome, proteome, metabolome and tissue-resident microbiome, bring newer opportunities for developing a more integrative insight into immunocellular mechanisms within different clinical contexts. The new ability to map the heterogeneity of composition, trajectory and endpoints of immune responses, in both health and disease, also necessitates incorporation into the potential standard model of immune functions, which again can only be achieved through multi-omics probing of immune responses and integrated analyses of the multi-dimensional data.
Collapse
Affiliation(s)
- Dipyaman Ganguly
- IICB-Translational Research Unit of Excellence, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| |
Collapse
|
2
|
Tawfeeq C, Song J, Khaniya U, Madej T, Wang J, Youkharibache P, Abrol R. Towards a structural and functional analysis of the immunoglobulin-fold proteome. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 138:135-178. [PMID: 38220423 DOI: 10.1016/bs.apcsb.2023.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
The immunoglobulin fold (Ig fold) domain is a super-secondary structural motif consisting of a sandwich with two layers of β-sheets that is present in many proteins with very diverse biological functions covering a wide range of physiological processes. This domain presents a modular architecture built with β strands connected by variable length loops that has a highly conserved structural core of four β-strands and quite variable β-sheet extensions in the two sandwich layers that enable both divergent and convergent evolutionary mechanisms in the known Ig fold proteome. The central role of this Ig fold's structural plasticity in the evolutionary success of antibodies in our immune system is well established. Nature has also utilized this Ig fold in all domains of life in many different physiological contexts that go way beyond the immune system. Here we will present a structural and functional overview of the utilization of the Ig fold in different biological processes and in different cellular contexts to highlight some of the innumerable ways that this structural motif can interact in multidomain proteins to enable their diversity of functions. This includes shareable specific protein structure visualizations behind those functions that serve as starting points for further explorations of the biomolecular interactions spanning the Ig fold proteome. This overview also highlights how this Ig fold is being utilized through natural adaptation, engineering, and even building from scratch for a range of biotechnological applications.
Collapse
Affiliation(s)
- Caesar Tawfeeq
- Department of Chemistry and Biochemistry, California State University Northridge, Northridge, United States
| | - James Song
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
| | - Umesh Khaniya
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Thomas Madej
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
| | - Jiyao Wang
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
| | - Philippe Youkharibache
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, United States.
| | - Ravinder Abrol
- Department of Chemistry and Biochemistry, California State University Northridge, Northridge, United States.
| |
Collapse
|
3
|
Crater JM, Dunn DC, Nixon DF, Furler O’Brien RL. A History and Atlas of the Human CD4 + T Helper Cell. Biomedicines 2023; 11:2608. [PMID: 37892982 PMCID: PMC10604283 DOI: 10.3390/biomedicines11102608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/12/2023] [Accepted: 09/18/2023] [Indexed: 10/29/2023] Open
Abstract
CD4+ T cells have orchestrated and regulated immunity since the introduction of jawed vertebrates, yet our understanding of CD4+ T cell evolution, development, and cellular physiology has only begun to be unearthed in the past few decades. Discoveries of genetic diseases that ablate this cellular population have provided insight into their critical functions while transcriptomics, proteomics, and high-resolution microscopy have recently revealed new insights into CD4+ T cell anatomy and physiology. This article compiles historical, microscopic, and multi-omics data that can be used as a reference atlas and index to dissect cellular physiology within these influential cells and further understand pathologies like HIV infection that inflict human CD4+ T cells.
Collapse
Affiliation(s)
| | | | | | - Robert L. Furler O’Brien
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, 413 E 69th St., Belfer Research Building, New York, NY 10021, USA
| |
Collapse
|
4
|
Devaux CA, Pontarotti P, Nehari S, Raoult D. 'Cannibalism' of exogenous DNA sequences: The ancestral form of adaptive immunity which entails recognition of danger. Front Immunol 2022; 13:989707. [PMID: 36618387 PMCID: PMC9816338 DOI: 10.3389/fimmu.2022.989707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Adaptive immunity is a sophisticated form of immune response capable of retaining the molecular memory of a very great diversity of target antigens (epitopes) as non-self. It is capable of reactivating itself upon a second encounter with an immunoglobulin or T-cell receptor antigen-binding site with a known epitope that had previously primed the host immune system. It has long been considered that adaptive immunity is a highly evolved form of non-self recognition that appeared quite late in speciation and complemented a more generalist response called innate immunity. Innate immunity offers a relatively non-specific defense (although mediated by sensors that could specifically recognize virus or bacteria compounds) and which does not retain a memory of the danger. But this notion of recent acquisition of adaptive immunity is challenged by the fact that another form of specific recognition mechanisms already existed in prokaryotes that may be able to specifically auto-protect against external danger. This recognition mechanism can be considered a primitive form of specific (adaptive) non-self recognition. It is based on the fact that many archaea and bacteria use a genome editing system that confers the ability to appropriate viral DNA sequences allowing prokaryotes to prevent host damage through a mechanism very similar to adaptive immunity. This is indistinctly called, 'endogenization of foreign DNA' or 'viral DNA predation' or, more pictorially 'DNA cannibalism'. For several years evidence has been accumulating, highlighting the crucial role of endogenization of foreign DNA in the fundamental processes related to adaptive immunity and leading to a change in the dogma that adaptive immunity appeared late in speciation.
Collapse
Affiliation(s)
- Christian A. Devaux
- Aix-Marseille University, Institut de recherche pour le développement (IRD), Assistance Publique Hôpitaux de Marseille (APHM), MEPHI, Institut Hospitalo-universitaire (IHU)-Méditerranée Infection, Marseille, France,Department of Biological Sciences, Centre National de la Recherche Scientifique, Centre National de la Recherche Scientifique (CNRS)-SNC5039, Marseille, France,*Correspondence: Christian A. Devaux,
| | - Pierre Pontarotti
- Aix-Marseille University, Institut de recherche pour le développement (IRD), Assistance Publique Hôpitaux de Marseille (APHM), MEPHI, Institut Hospitalo-universitaire (IHU)-Méditerranée Infection, Marseille, France,Department of Biological Sciences, Centre National de la Recherche Scientifique, Centre National de la Recherche Scientifique (CNRS)-SNC5039, Marseille, France
| | - Sephora Nehari
- Aix-Marseille University, Institut de recherche pour le développement (IRD), Assistance Publique Hôpitaux de Marseille (APHM), MEPHI, Institut Hospitalo-universitaire (IHU)-Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Aix-Marseille University, Institut de recherche pour le développement (IRD), Assistance Publique Hôpitaux de Marseille (APHM), MEPHI, Institut Hospitalo-universitaire (IHU)-Méditerranée Infection, Marseille, France
| |
Collapse
|
5
|
Bunnoy A, Na-Nakorn U, Srisapoome P. Mystifying Molecular Structure, Expression and Repertoire Diversity of IgM Heavy Chain Genes (Ighμ) in Clarias Catfish and Hybrids: Two Novel Transcripts in Vertebrates. Front Immunol 2022; 13:884434. [PMID: 35784299 PMCID: PMC9247300 DOI: 10.3389/fimmu.2022.884434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 05/12/2022] [Indexed: 11/16/2022] Open
Abstract
Two novel immunoglobulin heavy chain (Ighμ) transcripts encoding membrane-bound forms of IgM (mIgM) were discovered in bighead catfish, Clarias macrocephalus. The first transcript contains four constant and two transmembrane domains [Cμ1-Cμ2-Cμ3-Cμ4-TM1-TM2] that have never been reported in teleosts, and the second transcript is an unusual mIgM that has never been identified in any vertebrate [Cμ1-(Cδ2-Cδ3-Cδ4-Cδ5)-Cμ2-Cμ3-TM1-TM2]. Fluorescence in situ hybridization (FISH) in bighead catfish, North African catfish (C. gariepinus) and hybrid catfish revealed a single copy of Ighμ in individual parent catfish, while two gene copies were found in diploid hybrid catfish. Intensive sequence analysis demonstrated multiple distinct structural variabilities in the VH domain in Clarias, and hybrid catfish were defined and used to generate diversity with various mechanisms. Expression analysis of Ighμ in Aeromonas hydrophila infection of the head kidney, peripheral blood leukocytes and spleen revealed significantly higher levels in North African catfish and hybrid catfish than in bighead catfish.
Collapse
Affiliation(s)
- Anurak Bunnoy
- Laboratory of Aquatic Animal Health Management, Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand
- Center of Excellence in Aquatic Animal Health Management, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand
| | - Uthairat Na-Nakorn
- Laboratory of Aquatic Animal Genetics, Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand
- Academy of Science, The Royal Society of Thailand, Bangkok, Thailand
| | - Prapansak Srisapoome
- Laboratory of Aquatic Animal Health Management, Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand
- Center of Excellence in Aquatic Animal Health Management, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand
- *Correspondence: Prapansak Srisapoome,
| |
Collapse
|
6
|
Boraschi D. What Is IL-1 for? The Functions of Interleukin-1 Across Evolution. Front Immunol 2022; 13:872155. [PMID: 35464444 PMCID: PMC9020223 DOI: 10.3389/fimmu.2022.872155] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/11/2022] [Indexed: 11/13/2022] Open
Abstract
Interleukin-1 is a cytokine with potent inflammatory and immune-amplifying effects, mainly produced by macrophages during defensive reactions. In mammals, IL-1 is a superfamily of eleven structurally similar proteins, all involved in inflammation or its control, which mainly act through binding to specific receptors on the plasma membrane of target cells. IL-1 receptors are also a family of ten structurally similar transmembrane proteins that assemble in heterocomplexes. In addition to their innate immune/inflammatory effects, the physiological role of IL-1 family cytokines seems to be linked to the development of adaptive immunity in vertebrates. We will discuss why IL-1 developed in vertebrates and what is its physiological role, as a basis for understanding when and how it can be involved in the initiation and establishment of pathologies.
Collapse
Affiliation(s)
- Diana Boraschi
- Shenzhen Institute of Advanced Technology (SIAT), Chinese Academy of Science (CAS), Shenzhen, China.,Institute of Biochemistry and Cell Biology (IBBC), National Research Council (CNR), Napoli, Italy.,Stazione Zoologica Anton Dohrn, Napoli, Italy
| |
Collapse
|
7
|
Sherwood ER, Burelbach KR, McBride MA, Stothers CL, Owen AM, Hernandez A, Patil NK, Williams DL, Bohannon JK. Innate Immune Memory and the Host Response to Infection. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:785-792. [PMID: 35115374 PMCID: PMC8982914 DOI: 10.4049/jimmunol.2101058] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 12/09/2021] [Indexed: 01/02/2023]
Abstract
Unlike the adaptive immune system, the innate immune system has classically been characterized as being devoid of memory functions. However, recent research shows that innate myeloid and lymphoid cells have the ability to retain memory of prior pathogen exposure and become primed to elicit a robust, broad-spectrum response to subsequent infection. This phenomenon has been termed innate immune memory or trained immunity. Innate immune memory is induced via activation of pattern recognition receptors and the actions of cytokines on hematopoietic progenitors and stem cells in bone marrow and innate leukocytes in the periphery. The trained phenotype is induced and sustained via epigenetic modifications that reprogram transcriptional patterns and metabolism. These modifications augment antimicrobial functions, such as leukocyte expansion, chemotaxis, phagocytosis, and microbial killing, to facilitate an augmented host response to infection. Alternatively, innate immune memory may contribute to the pathogenesis of chronic diseases, such as atherosclerosis and Alzheimer's disease.
Collapse
Affiliation(s)
- Edward R Sherwood
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN;
- Department of Anesthesiology, Vanderbilt University Medical Center, Nashville, TN
- Department of Surgery, East Tennessee State University, Quillen College of Medicine, Johnson City, TN; and
- Center for Inflammation, Infectious Disease and Immunity, East Tennessee State University, Quillen College of Medicine, Johnson City, TN
| | | | - Margaret A McBride
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN
| | - Cody L Stothers
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN
| | - Allison M Owen
- Department of Anesthesiology, Vanderbilt University Medical Center, Nashville, TN
| | - Antonio Hernandez
- Department of Anesthesiology, Vanderbilt University Medical Center, Nashville, TN
| | - Naeem K Patil
- Department of Anesthesiology, Vanderbilt University Medical Center, Nashville, TN
| | - David L Williams
- Department of Surgery, East Tennessee State University, Quillen College of Medicine, Johnson City, TN; and
- Center for Inflammation, Infectious Disease and Immunity, East Tennessee State University, Quillen College of Medicine, Johnson City, TN
| | - Julia K Bohannon
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN
- Department of Anesthesiology, Vanderbilt University Medical Center, Nashville, TN
| |
Collapse
|
8
|
Evolution of variable lymphocyte receptor B antibody loci in jawless vertebrates. Proc Natl Acad Sci U S A 2021; 118:2116522118. [PMID: 34880135 DOI: 10.1073/pnas.2116522118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2021] [Indexed: 11/18/2022] Open
Abstract
Three types of variable lymphocyte receptor (VLR) genes, VLRA, VLRB, and VLRC, encode antigen recognition receptors in the extant jawless vertebrates, lampreys and hagfish. The somatically diversified repertoires of these VLRs are generated by serial stepwise copying of leucine-rich repeat (LRR) sequences into an incomplete germline VLR gene. Lymphocytes that express VLRA or VLRC are T cell-like, while VLRB-expressing cells are B cell-like. Here, we analyze the composition of the VLRB locus in different jawless vertebrates to elucidate its configuration and evolutionary modification. The incomplete germline VLRB genes of two hagfish species contain short noncoding intervening sequences, whereas germline VLRB genes in six representative lamprey species have much longer intervening sequences that exhibit notable genomic variation. Genomic clusters of potential LRR cassette donors, fragments of which are copied to complete VLRB gene assembly, are identified in Japanese lamprey and sea lamprey. In the sea lamprey, 428 LRR cassettes are located in five clusters spread over a total of 1.7 Mbp of chromosomal DNA. Preferential usage of the different donor cassettes for VLRB assemblage is characterized in our analysis, which reveals evolutionary modifications of the lamprey VLRB genes, elucidates the organization of the complex VLRB locus, and provides a comprehensive catalog of donor VLRB cassettes in sea lamprey and Japanese lamprey.
Collapse
|
9
|
Anumukonda K, Francis M, Currie P, Tulenko F, Hsu E. Heavy chain-only antibody genes in fish evolved to generate unique CDR3 repertoire. Eur J Immunol 2021; 52:247-260. [PMID: 34708869 DOI: 10.1002/eji.202149588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 10/08/2021] [Accepted: 10/26/2021] [Indexed: 11/11/2022]
Abstract
In addition to conventional immunoglobulin, camelids and cartilaginous fish express a special class of antibody that consists only of heavy (H) chain (HCAbs). In the holocephalan elephantfish, there are two HCAb classes, one of which has evolved surprising features. The H-chain genes in cartilaginous fish are organized as 20-200 minigenes, or clusters, each consisting of VH, 1-3 DH, JH gene segments with one set of constant region exons. We report that HHC2 (holocephalan H-chain antibody 2) evolved from IgM H-chain clusters, but its DH gene segments have diverged considerably. The three DH in HHC2 clusters are A-rich, so that one to three potential reading frames for each DH encode lysine and arginine. All three are incorporated into the rearranged VDJ, ensuring that the ligand-binding site carries multiple basic residues, as cDNA sequences demonstrate. The electropositive character in HHC2 CDR3 is accompanied by a paucity of aromatic amino acids, the latter feature at variance to the established, interactive role of tyrosine not only in ligand-binding but generally at interfaces of protein complexes. The selection for these divergent HHC2 features challenges currently accepted ideas on what determines antibody reactivity and molecular recognition.
Collapse
Affiliation(s)
- Kamala Anumukonda
- Department of Physiology and Pharmacology, State University of New York Downstate Health Sciences University, Brooklyn, NY, 11203, USA
| | - Malcolm Francis
- National Institute of Water and Atmospheric Research, Wellington, New Zealand
| | - Peter Currie
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, 3800, Australia
| | - Frank Tulenko
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, 3800, Australia
| | - Ellen Hsu
- Department of Physiology and Pharmacology, State University of New York Downstate Health Sciences University, Brooklyn, NY, 11203, USA
| |
Collapse
|
10
|
Giorgetti OB, Shingate P, O'Meara CP, Ravi V, Pillai NE, Tay BH, Prasad A, Iwanami N, Tan HH, Schorpp M, Venkatesh B, Boehm T. Antigen receptor repertoires of one of the smallest known vertebrates. SCIENCE ADVANCES 2021; 7:7/1/eabd8180. [PMID: 33523858 PMCID: PMC7775753 DOI: 10.1126/sciadv.abd8180] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 11/04/2020] [Indexed: 05/06/2023]
Abstract
The rules underlying the structure of antigen receptor repertoires are not yet fully defined, despite their enormous importance for the understanding of adaptive immunity. With current technology, the large antigen receptor repertoires of mice and humans cannot be comprehensively studied. To circumvent the problems associated with incomplete sampling, we have studied the immunogenetic features of one of the smallest known vertebrates, the cyprinid fish Paedocypris sp. "Singkep" ("minifish"). Despite its small size, minifish has the key genetic facilities characterizing the principal vertebrate lymphocyte lineages. As described for mammals, the frequency distributions of immunoglobulin and T cell receptor clonotypes exhibit the features of fractal systems, demonstrating that self-similarity is a fundamental property of antigen receptor repertoires of vertebrates, irrespective of body size. Hence, minifish achieve immunocompetence via a few thousand lymphocytes organized in robust scale-free networks, thereby ensuring immune reactivity even when cells are lost or clone sizes fluctuate during immune responses.
Collapse
Affiliation(s)
- Orlando B Giorgetti
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
| | - Prashant Shingate
- Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673, Singapore
| | - Connor P O'Meara
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
| | - Vydianathan Ravi
- Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673, Singapore
| | - Nisha E Pillai
- Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673, Singapore
| | - Boon-Hui Tay
- Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673, Singapore
| | - Aravind Prasad
- Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673, Singapore
| | - Norimasa Iwanami
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
| | - Heok Hui Tan
- Lee Kong Chian Natural History Museum, National University of Singapore, Singapore 117377, Singapore
| | - Michael Schorpp
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
| | - Byrappa Venkatesh
- Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673, Singapore.
| | - Thomas Boehm
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany.
| |
Collapse
|
11
|
Zhang W, Qin L, Cai X, Juma SN, Xu R, Wei L, Wu Y, Cui X, Chen G, Liu L, Lv Z, Jiang X. Sequence structure character of IgNAR Sec in whitespotted bamboo shark (Chiloscyllium plagiosum). FISH & SHELLFISH IMMUNOLOGY 2020; 102:140-144. [PMID: 32311460 DOI: 10.1016/j.fsi.2020.04.037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 04/11/2020] [Accepted: 04/16/2020] [Indexed: 06/11/2023]
Abstract
Whitespotted bamboo shark (Chiloscyllium plagiosum) is a demersal cartilaginous fish with an adaptive immune system founded upon immunoglobulins. In this manuscript, we characterize the IgNAR of the whitespotted bamboo shark. A newly discovered alternative splicing form of IgNAR Sec (IgNARshort (ΔC2-C3) Sec) was identified, in which the C1 domain was spliced directly to the C4 domain, the process resulted in a molecule containing three constant domains. However, a single unpaired cysteine remains in the highly flexible hinge region, contributing in the formation of an interchain disulfide bond. Two types of C1 domain were found, and the one lacking a short α-helix showed lower proportion. This finding suggests that short α-helices might be important to the stability of IgNAR. High-throughput sequencing revealed that the percentage of VNAR types significantly vary between the diverse species of sharks. The variable region of IgNAR (the VNAR) with small size and stabilization is a potential candidate for immunotherapeutic agents. The structure and stability analysis in this manuscript may be useful in future biomedical applications.
Collapse
Affiliation(s)
- Wenjie Zhang
- College of Life Sciences, Zhejiang Sci-Tech University, 310018, Hangzhou, China; Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
| | - Lanyi Qin
- College of Life Sciences, Zhejiang Sci-Tech University, 310018, Hangzhou, China; Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
| | - Xinyi Cai
- College of Life Sciences, Zhejiang Sci-Tech University, 310018, Hangzhou, China; Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
| | - Salma Nassor Juma
- College of Life Sciences, Zhejiang Sci-Tech University, 310018, Hangzhou, China; Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
| | - Rong Xu
- College of Life Sciences, Zhejiang Sci-Tech University, 310018, Hangzhou, China; Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
| | - Ling Wei
- College of Life Sciences, Zhejiang Sci-Tech University, 310018, Hangzhou, China; Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
| | - Yixin Wu
- College of Life Sciences, Zhejiang Sci-Tech University, 310018, Hangzhou, China; Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
| | - Xuan Cui
- College of Life Sciences, Zhejiang Sci-Tech University, 310018, Hangzhou, China; Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
| | - Guiqian Chen
- College of Life Sciences, Zhejiang Sci-Tech University, 310018, Hangzhou, China; Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
| | - Lili Liu
- College of Life Sciences, Zhejiang Sci-Tech University, 310018, Hangzhou, China; Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
| | - Zhengbing Lv
- College of Life Sciences, Zhejiang Sci-Tech University, 310018, Hangzhou, China; Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
| | - Xiaofeng Jiang
- College of Life Sciences, Zhejiang Sci-Tech University, 310018, Hangzhou, China; Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
| |
Collapse
|
12
|
Ott JA, Harrison J, Flajnik MF, Criscitiello MF. Nurse shark T-cell receptors employ somatic hypermutation preferentially to alter alpha/delta variable segments associated with alpha constant region. Eur J Immunol 2020; 50:1307-1320. [PMID: 32346855 DOI: 10.1002/eji.201948495] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 03/02/2020] [Accepted: 04/24/2020] [Indexed: 12/25/2022]
Abstract
In addition to canonical TCR and BCR, cartilaginous fish assemble noncanonical TCR that employ various B-cell components. For example, shark T cells associate alpha (TCR-α) or delta (TCR-δ) constant (C) regions with Ig heavy chain (H) variable (V) segments or TCR-associated Ig-like V (TAILV) segments to form chimeric IgV-TCR, and combine TCRδC with both Ig-like and TCR-like V segments to form the doubly rearranging NAR-TCR. Activation-induced (cytidine) deaminase-catalyzed somatic hypermutation (SHM), typically used for B-cell affinity maturation, also is used by TCR-α during selection in the shark thymus presumably to salvage failing receptors. Here, we found that the use of SHM by nurse shark TCR varies depending on the particular V segment or C region used. First, SHM significantly alters alpha/delta V (TCRαδV) segments using TCR αC but not δC. Second, mutation to IgHV segments associated with TCR δC was reduced compared to mutation to TCR αδV associated with TCR αC. Mutation was present but limited in V segments of all other TCR chains including NAR-TCR. Unexpectedly, we found preferential rearrangement of the noncanonical IgHV-TCRδC over canonical TCR αδV-TCRδC receptors. The differential use of SHM may reveal how activation-induced (cytidine) deaminase targets V regions.
Collapse
Affiliation(s)
- Jeannine A Ott
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Jenna Harrison
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Martin F Flajnik
- Department of Microbiology and Immunology, School of Medicine, University of Maryland at Baltimore, Baltimore, MD, USA
| | - Michael F Criscitiello
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA.,Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health Science Center, Texas A&M University, College Station, TX, USA
| |
Collapse
|
13
|
Development of a Monoclonal Antibody Specific to the IgM Heavy Chain of Bighead Catfish ( Clarias macrocephalus): A Biomolecular Tool for the Detection and Quantification of IgM Molecules and IgM + Cells in Clarias Catfish. Biomolecules 2020; 10:biom10040567. [PMID: 32272764 PMCID: PMC7226592 DOI: 10.3390/biom10040567] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 04/06/2020] [Accepted: 04/06/2020] [Indexed: 12/14/2022] Open
Abstract
Catfish is a commonly-cultivated freshwater fish in Thailand and many Southeast Asian countries. The molecular data obtained for the IgM heavy chain (IgMH) of catfish have been useful for distinguishing monoclonal antibodies (mAbs). A mAb specific to Cμ1 of the IgMH of catfish (IgMHCμ1 mAb) was developed in a rabbit model using sequence information from bighead catfish (Clarias macrocephalus). The IgMHCμ1 mAb strongly recognized the IgM heavy chain of the tested catfish, namely, bighead catfish, African catfish (Clarias gariepinus) and their hybrid (C. macrocephalus × C. gariepinus), in immunological Western blot analysis and competitive ELISAs. Additionally, the IgMHCμ1 mAb successfully recognized IgM+ cells by detecting IgM molecules in both secreted and membrane-bound forms in peripheral blood leukocytes (PBLs). The IgMHCμ1 mAb was further used to quantify the percentage of IgM+ cells among PBLs through flow cytophotometry. The IgM+ cell percentages of healthy bighead catfish, African catfish and their hybrid were 38.0–39.9%, 45.6–53.2%, and 58.7–60.0%, respectively. Furthermore, the IgMHCμ1 mAb showed no cross-reactivity with the IgM of zebrafish. These findings suggest that this mAb can be used as an immunological tool for monitoring the health, immune status, and immune development of cultivated Clarias catfish.
Collapse
|
14
|
Deiss TC, Breaux B, Ott JA, Daniel RA, Chen PL, Castro CD, Ohta Y, Flajnik MF, Criscitiello MF. Ancient Use of Ig Variable Domains Contributes Significantly to the TCRδ Repertoire. THE JOURNAL OF IMMUNOLOGY 2019; 203:1265-1275. [PMID: 31341077 DOI: 10.4049/jimmunol.1900369] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 07/01/2019] [Indexed: 01/05/2023]
Abstract
The loci encoding B and T cell Ag receptors are generally distinct in commonly studied mammals, with each receptor's gene segments limited to intralocus, cis chromosomal rearrangements. The nurse shark (Ginglymostoma cirratum) represents the oldest vertebrate class, the cartilaginous fish, with adaptive immunity provided via Ig and TCR lineages, and is one species among a growing number of taxa employing Ig-TCRδ rearrangements that blend these distinct lineages. Analysis of the nurse shark Ig-TCRδ repertoire found that these rearrangements possess CDR3 characteristics highly similar to canonical TCRδ rearrangements. Furthermore, the Ig-TCRδ rearrangements are expressed with TCRγ, canonically found in the TCRδ heterodimer. We also quantified BCR and TCR transcripts in the thymus for BCR (IgHV-IgHC), chimeric (IgHV-TCRδC), and canonical (TCRδV-TCRδC) transcripts, finding equivalent expression levels in both thymus and spleen. We also characterized the nurse shark TCRαδ locus with a targeted bacterial artifical chromosome sequencing approach and found that the TCRδ locus houses a complex of V segments from multiple lineages. An IgH-like V segment, nestled within the nurse shark TCRδ translocus, grouped with IgHV-like rearrangements we found expressed with TCRδ (but not IgH) rearrangements in our phylogenetic analysis. This distinct lineage of TCRδ-associated IgH-like V segments was termed "TAILVs." Our data illustrate a dynamic TCRδ repertoire employing TCRδVs, NARTCRVs, bona fide trans-rearrangements from shark IgH clusters, and a novel lineage in the TCRδ-associated Ig-like V segments.
Collapse
Affiliation(s)
- Thaddeus C Deiss
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843
| | - Breanna Breaux
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843
| | - Jeannine A Ott
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843
| | - Rebecca A Daniel
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843
| | - Patricia L Chen
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843
| | - Caitlin D Castro
- Department of Microbiology and Immunology, School of Medicine, University of Maryland at Baltimore, Baltimore, MD 21201; and
| | - Yuko Ohta
- Department of Microbiology and Immunology, School of Medicine, University of Maryland at Baltimore, Baltimore, MD 21201; and
| | - Martin F Flajnik
- Department of Microbiology and Immunology, School of Medicine, University of Maryland at Baltimore, Baltimore, MD 21201; and
| | - Michael F Criscitiello
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843; .,Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health Science Center, Texas A&M University, College Station, TX 77843
| |
Collapse
|
15
|
Arneson A, Ernst J. Systematic discovery of conservation states for single-nucleotide annotation of the human genome. Commun Biol 2019; 2:248. [PMID: 31286065 PMCID: PMC6606595 DOI: 10.1038/s42003-019-0488-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 05/30/2019] [Indexed: 12/12/2022] Open
Abstract
Comparative genomics sequence data is an important source of information for interpreting genomes. Genome-wide annotations based on this data have largely focused on univariate scores or binary elements of evolutionary constraint. Here we present a complementary whole genome annotation approach, ConsHMM, which applies a multivariate hidden Markov model to learn de novo 'conservation states' based on the combinatorial and spatial patterns of which species align to and match a reference genome in a multiple species DNA sequence alignment. We applied ConsHMM to a 100-way vertebrate sequence alignment to annotate the human genome at single nucleotide resolution into 100 conservation states. These states have distinct enrichments for other genomic information including gene annotations, chromatin states, repeat families, and bases prioritized by various variant prioritization scores. Constrained elements have distinct heritability partitioning enrichments depending on their conservation state assignment. ConsHMM conservation states are a resource for analyzing genomes and genetic variants.
Collapse
Affiliation(s)
- Adriana Arneson
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095 USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095 USA
| | - Jason Ernst
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095 USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095 USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at University of California, Los Angeles, Los Angeles, CA 90095 USA
- Computer Science Department, University of California, Los Angeles, Los Angeles, CA 90095 USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095 USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095 USA
| |
Collapse
|
16
|
Zhou H, Liu S, Yin X, Li Z, Yang Z, Zhou R. Molecular Origin of the Stability Difference in Four Shark IgNAR Constant Domains. Biophys J 2019; 116:1907-1917. [PMID: 31060814 DOI: 10.1016/j.bpj.2019.04.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 02/09/2019] [Accepted: 04/15/2019] [Indexed: 12/11/2022] Open
Abstract
Improving the stability of antibodies for manufacture and shelf life is one of the main focuses of antibody engineering. One stabilization strategy is to perform specific mutations in human antibodies based on highly stable antibodies in other species. To identify the key residues for mutagenesis, it is necessary to understand the roles of these residues in stabilizing the antibody. Here, we use molecular dynamics simulations to study the molecular origin of the four shark immunoglobulin new antigen receptors constant domains (C1-C4). According to the unfolding pathways and the conformational free energy surfaces in 8 M urea at 380 K, the C2 domain is the most stable, followed by C4, C1, and C3, which agrees with the experimental findings. The C1 and C3 domains follow a common unfolding pathway in which the unfolding starts from the edge strands, particularly strand g, and then gradually progresses to the inner strands. Detailed structural analysis of the C2 domain reveals a "sandwich-like" R339-E322-R341 salt-bridge cluster on strand g, which grants ultrahigh stability to the C2 domain. We further design two sets of mutations by mutating E322 to alanine or setting all atomic charges in E322 to zero to break the salt-bridge cluster in the C2 domain, which confirms the importance of the salt bridges in stability. In the C4 domain, the D80-K104 salt bridge on strand g also strengthens the stability. On the other hand, in the C1 and C3 domains, there is no salt bridge on strand g. In addition to the salt bridges, the overall hydrophobicity score of the hydrophobic core is also positively correlated with the domain stability. Our findings provide a detailed microscopic picture of the molecular origin of the four shark immunoglobulin new antigen receptors constant domains that not only explains the differences in their structural stability but also provides important insights into future antibody design.
Collapse
Affiliation(s)
- Hong Zhou
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu, China
| | - Shengtang Liu
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu, China
| | - Xiuhua Yin
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu, China
| | - Zengpeng Li
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen, Fujian, China
| | - Zaixing Yang
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu, China.
| | - Ruhong Zhou
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu, China; IBM Thomas J. Watson Research Center, Yorktown Heights, New York; Department of Chemistry, Columbia University, New York, New York.
| |
Collapse
|
17
|
Fu Y, Yang Z, Huang J, Cheng X, Wang X, Yang S, Ren L, Lian Z, Han H, Zhao Y. Identification of Two Nonrearranging IgSF Genes in Chicken Reveals a Novel Family of Putative Remnants of an Antigen Receptor Precursor. THE JOURNAL OF IMMUNOLOGY 2019; 202:1992-2004. [PMID: 30770416 DOI: 10.4049/jimmunol.1801305] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 01/22/2019] [Indexed: 11/19/2022]
Abstract
In this study, we identified a pair of nonrearranging VJ-joined Ig superfamily genes, termed putative remnants of an Ag receptor precursor (PRARP) genes, in chicken. Both genes encode a single V-set Ig domain consisting of a canonical J-like segment and a potential immunoreceptor tyrosine-based inhibitory or switch motif in the cytoplasmic region. In vitro experiments showed that both genes were expressed at the cell surface as membrane proteins, and their recombinant products formed a monomer and a disulfide-linked homodimer or a heterodimer. These two genes were mainly expressed in B and T cells and were upregulated in response to stimulation with poly(I:C) in vitro and vaccination in vivo. Orthologs of PRARP have been identified in bony fish, amphibians, reptiles, and other birds, and a V-C1 structure similar to that of Ig or TCR chains was found in all these genes, with the exception of those in avian species, which appear to contain degenerated C1 domains or divergent Ig domains. Phylogenetic analyses suggested that the newly discovered genes do not belong to any known immune receptor family and appear to be a novel gene family. Further elucidation of the functions of PRARP and their origin might provide significant insights into the evolution of the immune system of jawed vertebrates.
Collapse
Affiliation(s)
- Yanbin Fu
- State Key Laboratory of Agrobiotechnology, College of Biological Science, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, People's Republic of China
| | - Zhi Yang
- State Key Laboratory of Agrobiotechnology, College of Biological Science, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, People's Republic of China
| | - Jinwei Huang
- State Key Laboratory of Agrobiotechnology, College of Biological Science, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, People's Republic of China
| | - Xueqian Cheng
- State Key Laboratory of Agrobiotechnology, College of Biological Science, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, People's Republic of China
| | - Xifeng Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Science, Beijing 100101, People's Republic of China; and
| | - Shiping Yang
- State Key Laboratory of Agrobiotechnology, College of Biological Science, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, People's Republic of China
| | - Liming Ren
- State Key Laboratory of Agrobiotechnology, College of Biological Science, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, People's Republic of China
| | - Zhengxing Lian
- Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, People's Republic of China
| | - Haitang Han
- State Key Laboratory of Agrobiotechnology, College of Biological Science, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, People's Republic of China;
| | - Yaofeng Zhao
- State Key Laboratory of Agrobiotechnology, College of Biological Science, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, People's Republic of China;
| |
Collapse
|
18
|
Potential Human Health Applications from Marine Biomedical Research with Elasmobranch Fishes. FISHES 2018. [DOI: 10.3390/fishes3040047] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Members of the subclass of fishes collectively known as elasmobranchs (Class Chondrichthyes, Subclass Elasmobranchii) include sharks, skates, rays, guitarfish, and sawfish. Having diverged from the main line of vertebrate evolution some 400 million years ago, these fishes have continued to be successful in our ever-changing oceans. Much of their success must be attributed to their uncanny ability to remain healthy. Based on decades of basic research, some of their secrets may be very close to benefitting man. In this short review, some of the molecular and cellular biological areas that show promise for potential human applications are presented. With a brief background and current status of relevant research, these topics include development of new antibiotics and novel treatments for cancer, macular degeneration, viral pathogens, and Parkinson’s disease; potentially useful genomic information from shark transcriptomes; shark antibody-derived drug delivery systems; and immune cell-derived compounds as potential cancer therapeutic agents.
Collapse
|
19
|
FcαRI binding at the IgA1 C H2-C H3 interface induces long-range conformational changes that are transmitted to the hinge region. Proc Natl Acad Sci U S A 2018; 115:E8882-E8891. [PMID: 30181292 DOI: 10.1073/pnas.1807478115] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
IgA effector functions include proinflammatory immune responses triggered upon clustering of the IgA-specific receptor, FcαRI, by IgA immune complexes. FcαRI binds to the IgA1-Fc domain (Fcα) at the CH2-CH3 junction and, except for CH2 L257 and L258, all side-chain contacts are contributed by the CH3 domain. In this study, we used experimental and computational approaches to elucidate energetic and conformational aspects of FcαRI binding to IgA. The energetic contribution of each IgA residue in the binding interface was assessed by alanine-scanning mutagenesis and equilibrium surface plasmon resonance (SPR). As expected, hydrophobic residues central to the binding site have strong energetic contributions to the FcαRI:Fcα interaction. Surprisingly, individual mutation of CH2 residues L257 and L258, found at the periphery of the FcαRI binding site, dramatically reduced binding affinity. Comparison of antibody:receptor complexes involving IgA or its precursor IgY revealed a conserved receptor binding site at the CH2-CH3 junction (or its equivalent). Given the importance of residues near the CH2-CH3 junction, we used coarse-grained Langevin dynamics simulations to understand the functional dynamics in Fcα. Our simulations indicate that FcαRI binding, either in an asymmetric (1:1) or symmetric (2:1) complex with Fcα, propagated long-range conformational changes across the Fc domains, potentially impacting the hinge and Fab regions. Subsequent SPR experiments confirmed that FcαRI binding to the Fcα CH2-CH3 junction altered the kinetics of HAA lectin binding at the IgA1 hinge. Receptor-induced long-distance conformational transitions have important implications for the interaction of aberrantly glycosylated IgA1 with anti-glycan autoantibodies in IgA nephropathy.
Collapse
|
20
|
Guselnikov SV, Baranov KO, Najakshin AM, Mechetina LV, Chikaev NA, Makunin AI, Kulemzin SV, Andreyushkova DA, Stöck M, Wuertz S, Gessner J, Warren WC, Schartl M, Trifonov VA, Taranin AV. Diversity of Immunoglobulin Light Chain Genes in Non-Teleost Ray-Finned Fish Uncovers IgL Subdivision into Five Ancient Isotypes. Front Immunol 2018; 9:1079. [PMID: 29892283 PMCID: PMC5985310 DOI: 10.3389/fimmu.2018.01079] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 04/30/2018] [Indexed: 01/02/2023] Open
Abstract
The aim of this study was to fill important gaps in the evolutionary history of immunoglobulins by examining the structure and diversity of IgL genes in non-teleost ray-finned fish. First, based on the bioinformatic analysis of recent transcriptomic and genomic resources, we experimentally characterized the IgL genes in the chondrostean fish, Acipenser ruthenus (sterlet). We show that this species has three loci encoding IgL kappa-like chains with a translocon-type gene organization and a single VJC cluster, encoding homogeneous lambda-like light chain. In addition, sterlet possesses sigma-like VL and J-CL genes, which are transcribed separately and both encode protein products with cleavable leader peptides. The Acipenseriformes IgL dataset was extended by the sequences mined in the databases of species belonging to other non-teleost lineages of ray-finned fish: Holostei and Polypteriformes. Inclusion of these new data into phylogenetic analysis showed a clear subdivision of IgL chains into five groups. The isotype described previously as the teleostean IgL lambda turned out to be a kappa and lambda chain paralog that emerged before the radiation of ray-finned fish. We designate this isotype as lambda-2. The phylogeny also showed that sigma-2 IgL chains initially regarded as specific for cartilaginous fish are present in holosteans, polypterids, and even in turtles. We conclude that there were five ancient IgL isotypes, which evolved differentially in various lineages of jawed vertebrates.
Collapse
Affiliation(s)
- Sergey V. Guselnikov
- Laboratory of Immunogenetics, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Konstantin O. Baranov
- Laboratory of Immunogenetics, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Alexander M. Najakshin
- Laboratory of Immunogenetics, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Ludmila V. Mechetina
- Laboratory of Immunogenetics, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Nikolai A. Chikaev
- Laboratory of Immunogenetics, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Alexey I. Makunin
- Laboratory of Comparative Genomics, Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Sergey V. Kulemzin
- Laboratory of Immunogenetics, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Daria A. Andreyushkova
- Laboratory of Comparative Genomics, Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Sven Wuertz
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Jörn Gessner
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Wesley C. Warren
- School of Medicine, McDonnell Genome Institute, Washington University, St. Louis, MO, United States
| | - Manfred Schartl
- Department of Physiological Chemistry, Biocenter, University of Würzburg, Würzburg, Germany
- Department of Biology, Hagler Institute for Advanced Study, Texas A&M University, College Station, TX, United States
- Comprehensive Cancer Center Mainfranken, University Hospital Würzburg, Würzburg, Germany
| | - Vladimir A. Trifonov
- Novosibirsk State University, Novosibirsk, Russia
- Laboratory of Comparative Genomics, Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Alexander V. Taranin
- Laboratory of Immunogenetics, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| |
Collapse
|
21
|
Trautmann A. From kinetics and cellular cooperations to cancer immunotherapies. Oncotarget 2018; 7:44779-44789. [PMID: 27014912 PMCID: PMC5190134 DOI: 10.18632/oncotarget.8242] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 03/04/2016] [Indexed: 12/26/2022] Open
Abstract
In this review will be underlined two simple ideas of potential interest for the design of cancer immunotherapies. One concerns the importance of kinetics, with the key notion that a single cause may trigger two opposite effects with different kinetics. The importance of this phenomenon will be underlined in neurobiology, transcription networks and the immune system. The second idea is that efficient immune responses have been selected against pathogens, throughout evolution. They are never due to a single cell type, but always require multiple, complex cellular cooperations. One cannot recognize this fact and persist in the presently dominant T-cell centered view of cancer immunotherapies. Suggestions will be made to incorporate these simple ideas for improving these therapies.
Collapse
Affiliation(s)
- Alain Trautmann
- INSERM, U1016, Institut Cochin, Paris, France.,CNRS, UMR8104, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France.,Equipe Labellisée "Ligue contre le Cancer", Paris, France
| |
Collapse
|
22
|
Trapanese M, Buglione M, Maselli V, Petrelli S, Aceto S, Fulgione D. The first transcriptome of Italian wall lizard, a new tool to infer about the Island Syndrome. PLoS One 2017; 12:e0185227. [PMID: 28953924 PMCID: PMC5617171 DOI: 10.1371/journal.pone.0185227] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 09/09/2017] [Indexed: 12/04/2022] Open
Abstract
Some insular lizards show a high degree of differentiation from their conspecific mainland populations, like Licosa island lizards, which are described as affected by Reversed Island Syndrome (RIS). In previous works, we demonstrated that some traits of RIS, as melanization, depend on a differential expression of gene encoding melanocortin receptors. To better understand the basis of syndrome, and providing raw data for future investigations, we generate the first de novo transcriptome of the Italian wall lizard. Comparing mainland and island transcriptomes, we link differences in life-traits to differential gene expression. Our results, taking together testis and brain sequences, generated 275,310 and 269,885 transcripts, 18,434 and 21,606 proteins in Gene Ontology annotation, for mainland and island respectively. Variant calling analysis identified about the same number of SNPs in island and mainland population. Instead, through a differential gene expression analysis we found some putative genes involved in syndrome more expressed in insular samples like Major Histocompatibility Complex class I, Immunoglobulins, Melanocortin 4 receptor, Neuropeptide Y and Proliferating Cell Nuclear Antigen.
Collapse
Affiliation(s)
- Martina Trapanese
- Department of Biology, University of Naples Federico II, campus of Monte Sant’Angelo, Naples, Italy
| | - Maria Buglione
- Department of Biology, University of Naples Federico II, campus of Monte Sant’Angelo, Naples, Italy
| | - Valeria Maselli
- Department of Biology, University of Naples Federico II, campus of Monte Sant’Angelo, Naples, Italy
| | - Simona Petrelli
- Department of Biology, University of Naples Federico II, campus of Monte Sant’Angelo, Naples, Italy
| | - Serena Aceto
- Department of Biology, University of Naples Federico II, campus of Monte Sant’Angelo, Naples, Italy
| | - Domenico Fulgione
- Department of Biology, University of Naples Federico II, campus of Monte Sant’Angelo, Naples, Italy
- * E-mail:
| |
Collapse
|
23
|
Iacoangeli A, Lui A, Haines A, Ohta Y, Flajnik M, Hsu E. Evidence for Ig Light Chain Isotype Exclusion in Shark B Lymphocytes Suggests Ordered Mechanisms. THE JOURNAL OF IMMUNOLOGY 2017; 199:1875-1885. [PMID: 28760881 DOI: 10.4049/jimmunol.1700762] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 06/27/2017] [Indexed: 01/06/2023]
Abstract
Unlike most vertebrates, the shark IgL gene organization precludes secondary rearrangements that delete self-reactive VJ rearranged genes. Nurse sharks express four L chain isotypes, κ, λ, σ, and σ-2, encoded by 35 functional minigenes or clusters. The sequence of gene activation/expression and receptor editing of these isotypes have not been studied. We therefore investigated the extent of isotypic exclusion in separated B cell subpopulations. Surface Ig (sIg)κ-expressing cells, isolated with mAb LK14 that recognizes Cκ, carry predominantly nonproductive rearrangements of other L chain isotypes. Conversely, after depletion with LK14, sIgM+ cells contained largely nonproductive κ and enrichment for in-frame VJ of the others. Because some isotypic inclusion was observed at the mRNA level, expression in the BCR was examined. Functional λ mRNA was obtained, as expected, from the LK14-depleted population, but was also in sIgκ+ splenocytes. Whereas λ somatic mutants from the depleted sample displayed evidence of positive selection, the λ genes in sIgκ+ cells accumulated bystander mutations indicating a failure to express their products at the cell surface in association with the BCR H chain. In conclusion, a shark B cell expresses one L chain isotype at the surface and other isotypes as nonproductive VJ, sterile transcripts, or in-frame VJ whose products may not associate with the H chain. Based on the mRNA content found in the B cell subpopulations, an order of L chain gene activation is suggested as: σ-2 followed by κ, then σ and λ.
Collapse
Affiliation(s)
- Anna Iacoangeli
- Tisch Multiple Sclerosis Research Center of New York, New York, NY 10019
| | - Anita Lui
- Department of Physiology and Pharmacology, State University of New York Health Science Center at Brooklyn, Brooklyn, NY 11203; and
| | - Ashley Haines
- Department of Microbiology and Immunology, University of Maryland Baltimore, Baltimore, MD 21201
| | - Yuko Ohta
- Department of Microbiology and Immunology, University of Maryland Baltimore, Baltimore, MD 21201
| | - Martin Flajnik
- Department of Microbiology and Immunology, University of Maryland Baltimore, Baltimore, MD 21201
| | - Ellen Hsu
- Department of Physiology and Pharmacology, State University of New York Health Science Center at Brooklyn, Brooklyn, NY 11203; and
| |
Collapse
|
24
|
Hsu E. Assembly and Expression of Shark Ig Genes. THE JOURNAL OF IMMUNOLOGY 2017; 196:3517-23. [PMID: 27183649 DOI: 10.4049/jimmunol.1600164] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 03/04/2016] [Indexed: 11/19/2022]
Abstract
Sharks are modern descendants of the earliest vertebrates possessing Ig superfamily receptor-based adaptive immunity. They respond to immunogen with Abs that, upon boosting, appear more rapidly and show affinity maturation. Specific Abs and immunological memory imply that Ab diversification and clonal selection exist in cartilaginous fish. Shark Ag receptors are generated through V(D)J recombination, and because it is a mechanism known to generate autoreactive receptors, this implies that shark lymphocytes undergo selection. In the mouse, the ∼2.8-Mb IgH and IgL loci require long-range, differential activation of component parts for V(D)J recombination, allelic exclusion, and receptor editing. These processes, including class switching, evolved with and appear inseparable from the complex locus organization. In contrast, shark Igs are encoded by 100-200 autonomously rearranging miniloci. This review describes how the shark primary Ab repertoire is generated in the absence of structural features considered essential in mammalian Ig gene assembly and expression.
Collapse
Affiliation(s)
- Ellen Hsu
- Department of Physiology and Pharmacology, The State University of New York Health Science Center at Brooklyn, Brooklyn, NY 11203
| |
Collapse
|
25
|
Ferrara JL, Smith CM, Sheets J, Reddy P, Serody JS. Altered homeostatic regulation of innate and adaptive immunity in lower gastrointestinal tract GVHD pathogenesis. J Clin Invest 2017; 127:2441-2451. [PMID: 28581444 DOI: 10.1172/jci90592] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Lower gastrointestinal (GI) tract graft-versus-host disease (GVHD) is the predominant cause of morbidity and mortality from GVHD after allogeneic stem cell transplantation. Recent data indicate that lower GI tract GVHD is a complicated process mediated by donor/host antigenic disparities. This process is exacerbated by significant changes to the microbiome, and innate and adaptive immune responses that are critical to the induction of disease, persistence of inflammation, and a lack of response to therapy. Here, we discuss new insights into the biology of lower GI tract GVHD and focus on intrinsic pathways and regulatory mechanisms crucial to normal intestinal function. We then describe multiple instances in which these homeostatic mechanisms are altered by donor T cells or conditioning therapy, resulting in exacerbation of GVHD. We also discuss data suggesting that some of these mechanisms produce biomarkers that could be informative as to the severity of GVHD and its response to therapy. Finally, novel therapies that might restore homeostasis in the GI tract during GVHD are highlighted.
Collapse
Affiliation(s)
- James Lm Ferrara
- Departments of Medicine, Pediatrics, and Academic Informatics and Technology, Icahn School of Medicine at Mount Sinai and Tisch Cancer Institute, New York, New York, USA
| | - Christopher M Smith
- Departments of Medicine, Pediatrics, and Academic Informatics and Technology, Icahn School of Medicine at Mount Sinai and Tisch Cancer Institute, New York, New York, USA
| | - Julia Sheets
- University of North Carolina Hospital, Chapel Hill, North Carolina, USA
| | - Pavan Reddy
- Department of Medicine and University of Michigan Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
| | - Jonathan S Serody
- Department of Medicine and UNC Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| |
Collapse
|
26
|
Rouet R, Langley DB, Schofield P, Christie M, Roome B, Porebski BT, Buckle AM, Clifton BE, Jackson CJ, Stock D, Christ D. Structural reconstruction of protein ancestry. Proc Natl Acad Sci U S A 2017; 114:3897-3902. [PMID: 28356519 PMCID: PMC5393204 DOI: 10.1073/pnas.1613477114] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ancestral protein reconstruction allows the resurrection and characterization of ancient proteins based on computational analyses of sequences of modern-day proteins. Unfortunately, many protein families are highly divergent and not suitable for sequence-based reconstruction approaches. This limitation is exemplified by the antigen receptors of jawed vertebrates (B- and T-cell receptors), heterodimers formed by pairs of Ig domains. These receptors are believed to have evolved from an extinct homodimeric ancestor through a process of gene duplication and diversification; however molecular evidence has so far remained elusive. Here, we use a structural approach and laboratory evolution to reconstruct such molecules and characterize their interaction with antigen. High-resolution crystal structures of reconstructed homodimeric receptors in complex with hen-egg white lysozyme demonstrate how nanomolar affinity binding of asymmetrical antigen is enabled through selective recruitment and structural plasticity within the receptor-binding site. Our results provide structural evidence in support of long-held theories concerning the evolution of antigen receptors, and provide a blueprint for the experimental reconstruction of protein ancestry in the absence of phylogenetic evidence.
Collapse
Affiliation(s)
- Romain Rouet
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
- Faculty of Medicine, St. Vincent's Clinical School, University of New South Wales, Darlinghurst, Sydney, NSW 2010, Australia
| | - David B Langley
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, NSW 2010, Australia
| | - Peter Schofield
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
- Faculty of Medicine, St. Vincent's Clinical School, University of New South Wales, Darlinghurst, Sydney, NSW 2010, Australia
| | - Mary Christie
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
- Faculty of Medicine, St. Vincent's Clinical School, University of New South Wales, Darlinghurst, Sydney, NSW 2010, Australia
| | - Brendan Roome
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
- Faculty of Medicine, St. Vincent's Clinical School, University of New South Wales, Darlinghurst, Sydney, NSW 2010, Australia
| | - Benjamin T Porebski
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Ashley M Buckle
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Ben E Clifton
- Research School of Chemistry, Australian National University, Acton, ACT 2601, Australia
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Acton, ACT 2601, Australia
| | - Daniela Stock
- Faculty of Medicine, St. Vincent's Clinical School, University of New South Wales, Darlinghurst, Sydney, NSW 2010, Australia
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, NSW 2010, Australia
| | - Daniel Christ
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia;
- Faculty of Medicine, St. Vincent's Clinical School, University of New South Wales, Darlinghurst, Sydney, NSW 2010, Australia
| |
Collapse
|
27
|
Marra NJ, Richards VP, Early A, Bogdanowicz SM, Pavinski Bitar PD, Stanhope MJ, Shivji MS. Comparative transcriptomics of elasmobranchs and teleosts highlight important processes in adaptive immunity and regional endothermy. BMC Genomics 2017; 18:87. [PMID: 28132643 PMCID: PMC5278576 DOI: 10.1186/s12864-016-3411-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 12/12/2016] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Comparative genomic and/or transcriptomic analyses involving elasmobranchs remain limited, with genome level comparisons of the elasmobranch immune system to that of higher vertebrates, non-existent. This paper reports a comparative RNA-seq analysis of heart tissue from seven species, including four elasmobranchs and three teleosts, focusing on immunity, but concomitantly seeking to identify genetic similarities shared by the two lamnid sharks and the single billfish in our study, which could be linked to convergent evolution of regional endothermy. RESULTS Across seven species, we identified an average of 10,877 Swiss-Prot annotated genes from an average of 32,474 open reading frames within each species' heart transcriptome. About half of these genes were shared between all species while the remainder included functional differences between our groups of interest (elasmobranch vs. teleost and endotherms vs. ectotherms) as revealed by Gene Ontology (GO) and selection analyses. A repeatedly represented functional category, in both the uniquely expressed elasmobranch genes (total of 259) and the elasmobranch GO enrichment results, involved antibody-mediated immunity, either in the recruitment of immune cells (Fc receptors) or in antigen presentation, including such terms as "antigen processing and presentation of exogenous peptide antigen via MHC class II", and such genes as MHC class II, HLA-DPB1. Molecular adaptation analyses identified three genes in elasmobranchs with a history of positive selection, including legumain (LGMN), a gene with roles in both innate and adaptive immunity including producing antigens for presentation by MHC class II. Comparisons between the endothermic and ectothermic species revealed an enrichment of GO terms associated with cardiac muscle contraction in endotherms, with 19 genes expressed solely in endotherms, several of which have significant roles in lipid and fat metabolism. CONCLUSIONS This collective comparative evidence provides the first multi-taxa transcriptomic-based perspective on differences between elasmobranchs and teleosts, and suggests various unique features associated with the adaptive immune system of elasmobranchs, pointing in particular to the potential importance of MHC Class II. This in turn suggests that expanded comparative work involving additional tissues, as well as genome sequencing of multiple elasmobranch species would be productive in elucidating the regulatory and genome architectural hallmarks of elasmobranchs.
Collapse
Affiliation(s)
- Nicholas J Marra
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA.,Save Our Seas Shark Research Center and Guy Harvey Research Institute, Nova Southeastern University, 8000 North Ocean Drive, Dania Beach, FL, 33004, USA
| | - Vincent P Richards
- Department of Biological Sciences, Clemson University, Clemson, SC, 29634, USA
| | - Angela Early
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Steve M Bogdanowicz
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Paulina D Pavinski Bitar
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Michael J Stanhope
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA.
| | - Mahmood S Shivji
- Save Our Seas Shark Research Center and Guy Harvey Research Institute, Nova Southeastern University, 8000 North Ocean Drive, Dania Beach, FL, 33004, USA.
| |
Collapse
|
28
|
Immunoglobulin light chain (IGL) genes in torafugu: Genomic organization and identification of a third teleost IGL isotype. Sci Rep 2017; 7:40416. [PMID: 28098239 PMCID: PMC5241823 DOI: 10.1038/srep40416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 12/06/2016] [Indexed: 02/05/2023] Open
Abstract
Here, we report a genome-wide survey of immunoglobulin light chain (IGL) genes of torafugu (Takifugu rubripes) revealing multi-clusters spanning three separate chromosomes (v5 assembly) and 45 scaffolds (v4 assembly). Conventional sequence similarity searches and motif scanning approaches based on recombination signal sequence (RSS) motifs were used. We found that three IGL isotypes (L1, L2, and L3) exist in torafugu and that several loci for each isotype are present. The transcriptional orientations of the variable IGL (VL) segments were found to be either the same (in the L2 isotype) or opposite (in the L1 and L3 isotypes) to the IGL joining (JL) and constant (CL) segments, suggesting they can undergo rearrangement by deletion or inversion when expressed. Alignments of expressed sequence tags (ESTs) to corresponding germline gene segments revealed expression of the three IGL isotypes in torafugu. Taken together, our findings provide a genomic framework for torafugu IGL genes and show that the IG diversity of this species could be attributed to at least three distinct chromosomal regions.
Collapse
|
29
|
Edholm ES, Banach M, Robert J. Evolution of innate-like T cells and their selection by MHC class I-like molecules. Immunogenetics 2016; 68:525-36. [PMID: 27368412 DOI: 10.1007/s00251-016-0929-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 06/22/2016] [Indexed: 11/28/2022]
Abstract
Until recently, major histocompatibility complex (MHC) class I-like-restricted innate-like αβT (iT) cells expressing an invariant or semi-invariant T cell receptor (TCR) repertoire were thought to be a recent evolutionary acquisition restricted to mammals. However, molecular and functional studies in Xenopus laevis have demonstrated that iT cells, defined as MHC class I-like-restricted innate-like αβT cells with a semi-invariant TCR, are evolutionarily conserved and prominent from early development in amphibians. As these iT cells lack the specificity conferred by conventional αβ TCRs, it is generally considered that they are specialized to recognize conserved antigens equivalent to pathogen-associated molecular patterns. Thus, one advantage offered by the MHC class I-like iT cell-based recognition system is that it can be adapted to a common pathogen and function on the basis of a relatively small number of T cells. Although iT cells have only been functionally described in mammals and amphibians, the identification of non-classical MHC/MHC class I-like genes in other groups of endothermic and ectothermic vertebrates suggests that iT cells have a broader phylogenetic distribution than previously envisioned. In this review, we discuss the possible role of iT cells during the emergence of the jawed vertebrate adaptive immune system.
Collapse
Affiliation(s)
- Eva-Stina Edholm
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Maureen Banach
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Jacques Robert
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, 14642, USA.
| |
Collapse
|
30
|
Guan X, Wang J, Ma L, Wang X, Cheng X, Han H, Zhao Y, Ren L. Multiple germline functional VL genes contribute to the IgL repertoire in ducks. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2016; 60:167-179. [PMID: 26945621 DOI: 10.1016/j.dci.2016.02.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 02/29/2016] [Accepted: 02/29/2016] [Indexed: 06/05/2023]
Abstract
In the immunoglobulin light chain gene loci of nearly all bird species examined to date, there is only a single functional variable gene segment that can recombine with joining gene segments. Thus, Ig light chain diversity relies on gene conversion using pseudogenes as sequence donors to modify the single rearranged variable gene. In the present study, we have sequenced a bacterial artificial chromosome (BAC) clone containing the entire duck Igλ light chain gene locus. Although only a single pair of Jλ and Cλ was found, 88 Vλ gene segments were identified upstream of the Jλ and Cλ segments. Among the identified Vλ gene segments, 79 appear to be pseudogenes, the remaining 9 are structurally intact and all are able to functionally rearrange with the Jλ. Phylogenetic analyses suggest that the 9 functional variable genes may have been derived from a single gene through duplication events. Although these multiple functional variable gene segments can be subject to VJ recombination, both gene conversion and somatic hypermutation are also actively involved in the generation of diversity in duck Igλ light chains. These data provide significant insight into understanding the duck Ig system.
Collapse
Affiliation(s)
- Xiaoxing Guan
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, PR China
| | - Jing Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, PR China
| | - Li Ma
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, PR China
| | - Xifeng Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, PR China
| | - Xueqian Cheng
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, PR China
| | - Haitang Han
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, PR China
| | - Yaofeng Zhao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, PR China
| | - Liming Ren
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, PR China
| |
Collapse
|
31
|
Generation of Anti-Boa Immunoglobulin Antibodies for Serodiagnostic Applications, and Their Use to Detect Anti-Reptarenavirus Antibodies in Boa Constrictor. PLoS One 2016; 11:e0158417. [PMID: 27355360 PMCID: PMC4927170 DOI: 10.1371/journal.pone.0158417] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 06/15/2016] [Indexed: 11/19/2022] Open
Abstract
Immunoglobulins (Igs), the key effectors of the adaptive immune system, mediate the specific recognition of foreign structures, i.e. antigens. In mammals, IgM production commonly precedes the production of IgG in the response to an infection. The reptilian counterpart of IgG is IgY, but the exact kinetics of the reptilian immune response are less well known. Boid inclusion body disease (BIBD), an often fatal disease of captive boas and pythons has been linked to reptarenavirus infection, and BIBD is believed to be immunosuppressive. However, so far, the study of the serological response towards reptarenaviruses in BIBD has been hampered by the lack of reagents. Thus we set up a purification protocol for boa constrictor IgY and IgM, which should also be applicable for other snake species. We used centrifugal filter units, poly ethylene glycol precipitation and gel permeation chromatography to purify and separate the IgM and IgY fractions from boa constrictor serum, which we further used to immunise rabbits. We affinity purified IgM and IgY specific reagents from the produced antiserum, and labelled the reagents with horseradish peroxidase. Finally, using the sera of snakes with known exposure to reptarenaviruses we demonstrated that the newly generated reagents can be utilised for serodiagnostic purposes, such as immunoblotting and immunofluorescent staining. To our knowledge, this is the first report to show reptarenavirus-specific antibodies in boa constrictors.
Collapse
|
32
|
Han B, Yuan H, Wang T, Li B, Ma L, Yu S, Huang T, Li Y, Fang D, Chen X, Wang Y, Qiu S, Guo Y, Fei J, Ren L, Pan-Hammarström Q, Hammarström L, Wang J, Wang J, Hou Y, Pan Q, Xu X, Zhao Y. Multiple IgH Isotypes Including IgD, Subclasses of IgM, and IgY Are Expressed in the Common Ancestors of Modern Birds. THE JOURNAL OF IMMUNOLOGY 2016; 196:5138-47. [PMID: 27183632 DOI: 10.4049/jimmunol.1600307] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 04/14/2016] [Indexed: 12/23/2022]
Abstract
Although evolutionarily just as ancient as IgM, it has been thought for many years that IgD is not present in birds. Based on the recently sequenced genomes of 48 bird species as well as high-throughput transcriptome sequencing of immune-related tissues, we demonstrate in this work that the ostrich (Struthio camelus) possesses a functional δ gene that encodes a membrane-bound IgD H chain with seven CH domains. Furthermore, δ sequences were clearly identified in many other bird species, demonstrating that the δ gene is widely distributed among birds and is only absent in certain bird species. We also show that the ostrich possesses two μ genes (μ1, μ2) and two υ genes (υ1, υ2), in addition to the δ and α genes. Phylogenetic analyses suggest that subclass diversification of both the μ and υ genes occurred during the early stages of bird evolution, after their divergence from nonavian reptiles. Although the positions of the two υ genes are unknown, physical mapping showed that the remaining genes are organized in the order μ1-δ-α-μ2, with the α gene being inverted relative to the others. Together with previous studies, our data suggest that birds and nonavian reptile species most likely shared a common ancestral IgH gene locus containing a δ gene and an inverted α gene. The δ gene was then evolutionarily lost in selected birds, whereas the α gene lost in selected nonavian reptiles. The data obtained in this study provide significant insights into the understanding of IgH gene evolution in tetrapods.
Collapse
Affiliation(s)
- Binyue Han
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, People's Republic of China
| | - Hui Yuan
- BGI-Shenzhen, Shenzhen 518083, People's Republic of China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Tao Wang
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, People's Republic of China
| | - Bo Li
- BGI-Shenzhen, Shenzhen 518083, People's Republic of China
| | - Li Ma
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, People's Republic of China
| | - Shuyang Yu
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, People's Republic of China
| | - Tian Huang
- School of Life Science, Henan University, Kaifeng 475004, People's Republic of China
| | - Yan Li
- Key Laboratory of Animal Reproduction and Germplasm Enhancement in Universities of Shandong, Qingdao Agricultural University, Qingdao 266109, People's Republic of China; and
| | - Dongming Fang
- BGI-Shenzhen, Shenzhen 518083, People's Republic of China
| | - Xiaoli Chen
- BGI-Shenzhen, Shenzhen 518083, People's Republic of China
| | - Yongsi Wang
- BGI-Shenzhen, Shenzhen 518083, People's Republic of China
| | - Si Qiu
- BGI-Shenzhen, Shenzhen 518083, People's Republic of China
| | - Ying Guo
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, People's Republic of China
| | - Jing Fei
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, People's Republic of China
| | - Liming Ren
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, People's Republic of China
| | - Qiang Pan-Hammarström
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska University Hospital Huddinge, SE-141 86, Stockholm, Sweden
| | - Lennart Hammarström
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska University Hospital Huddinge, SE-141 86, Stockholm, Sweden
| | - Jun Wang
- BGI-Shenzhen, Shenzhen 518083, People's Republic of China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen 518083, People's Republic of China
| | - Yong Hou
- BGI-Shenzhen, Shenzhen 518083, People's Republic of China
| | - Qingjie Pan
- Key Laboratory of Animal Reproduction and Germplasm Enhancement in Universities of Shandong, Qingdao Agricultural University, Qingdao 266109, People's Republic of China; and
| | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, People's Republic of China;
| | - Yaofeng Zhao
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, People's Republic of China;
| |
Collapse
|
33
|
A Comprehensive Analysis of the Phylogeny, Genomic Organization and Expression of Immunoglobulin Light Chain Genes in Alligator sinensis, an Endangered Reptile Species. PLoS One 2016; 11:e0147704. [PMID: 26901135 PMCID: PMC4762898 DOI: 10.1371/journal.pone.0147704] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 01/07/2016] [Indexed: 12/02/2022] Open
Abstract
Crocodilians are evolutionarily distinct reptiles that are distantly related to lizards and are thought to be the closest relatives of birds. Compared with birds and mammals, few studies have investigated the Ig light chain of crocodilians. Here, employing an Alligator sinensis genomic bacterial artificial chromosome (BAC) library and available genome data, we characterized the genomic organization of the Alligator sinensis IgL gene loci. The Alligator sinensis has two IgL isotypes, λ and κ, the same as Anolis carolinensis. The Igλ locus contains 6 Cλ genes, each preceded by a Jλ gene, and 86 potentially functional Vλ genes upstream of (Jλ-Cλ)n. The Igκ locus contains a single Cκ gene, 6 Jκs and 62 functional Vκs. All VL genes are classified into a total of 31 families: 19 Vλ families and 12 Vκ families. Based on an analysis of the chromosomal location of the light chain genes among mammals, birds, lizards and frogs, the data further confirm that there are two IgL isotypes in the Alligator sinensis: Igλ and Igκ. By analyzing the cloned Igλ/κ cDNA, we identified a biased usage pattern of V families in the expressed Vλ and Vκ. An analysis of the junctions of the recombined VJ revealed the presence of N and P nucleotides in both expressed λ and κ sequences. Phylogenetic analysis of the V genes revealed V families shared by mammals, birds, reptiles and Xenopus, suggesting that these conserved V families are orthologous and have been retained during the evolution of IgL. Our data suggest that the Alligator sinensis IgL gene repertoire is highly diverse and complex and provide insight into immunoglobulin gene evolution in vertebrates.
Collapse
|
34
|
Iacoangeli A, Lui A, Naik U, Ohta Y, Flajnik M, Hsu E. Biased Immunoglobulin Light Chain Gene Usage in the Shark. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2015; 195:3992-4000. [PMID: 26342033 PMCID: PMC4592821 DOI: 10.4049/jimmunol.1501426] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 08/04/2015] [Indexed: 12/13/2022]
Abstract
This study of a large family of κ L chain clusters in nurse shark completes the characterization of its classical Ig gene content (two H chain isotypes, μ and ω, and four L chain isotypes, κ, λ, σ, and σ-2). The shark κ clusters are minigenes consisting of a simple VL-JL-CL array, where V to J recombination occurs over an ~500-bp interval, and functional clusters are widely separated by at least 100 kb. Six out of ~39 κ clusters are prerearranged in the germline (germline joined). Unlike the complex gene organization and multistep assembly process of Ig in mammals, each shark Ig rearrangement, somatic or in the germline, appears to be an independent event localized to the minigene. This study examined the expression of functional, nonproductive, and sterile transcripts of the κ clusters compared with the other three L chain isotypes. κ cluster usage was investigated in young sharks, and a skewed pattern of split gene expression was observed, one similar in functional and nonproductive rearrangements. These results show that the individual activation of the spatially distant κ clusters is nonrandom. Although both split and germline-joined κ genes are expressed, the latter are prominent in young animals and wane with age. We speculate that, in the shark, the differential activation of the multiple isotypes can be advantageously used in receptor editing.
Collapse
Affiliation(s)
- Anna Iacoangeli
- Department of Physiology and Pharmacology, State University of New York Health Science Center at Brooklyn, Brooklyn, NY 11203; and
| | - Anita Lui
- Department of Physiology and Pharmacology, State University of New York Health Science Center at Brooklyn, Brooklyn, NY 11203; and
| | - Ushma Naik
- Department of Physiology and Pharmacology, State University of New York Health Science Center at Brooklyn, Brooklyn, NY 11203; and
| | - Yuko Ohta
- Department of Microbiology and Immunology, University of Maryland, Baltimore, MD 21201
| | - Martin Flajnik
- Department of Microbiology and Immunology, University of Maryland, Baltimore, MD 21201
| | - Ellen Hsu
- Department of Physiology and Pharmacology, State University of New York Health Science Center at Brooklyn, Brooklyn, NY 11203; and
| |
Collapse
|
35
|
VNARs: An Ancient and Unique Repertoire of Molecules That Deliver Small, Soluble, Stable and High Affinity Binders of Proteins. Antibodies (Basel) 2015. [DOI: 10.3390/antib4030240] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
|
36
|
Middleton DMRL, Nelson NJ, Gartrell BD, La Flamme AC. Presence of antibodies to Salmonella in tuatara (Sphenodon punctatus) sera. Comp Immunol Microbiol Infect Dis 2015; 41:17-27. [PMID: 26264523 DOI: 10.1016/j.cimid.2015.06.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 06/11/2015] [Accepted: 06/11/2015] [Indexed: 10/23/2022]
Abstract
Colonisation of a host by pathogenic microorganisms is a near constant threat to the health of all vertebrates and most species have evolved an efficient adaptive immune response which produces antibodies following exposure to a specific antigen. The strength of this response can be influenced by many factors including sex and season. Tuatara are exposed to Salmonella through contact with infected skinks and soil; however, no gastrointestinal colonisation of tuatara with Salmonella has been found. Using Western blot and flow cytometry we have demonstrated that tuatara possess antibodies which recognise Salmonella antigens, but many of these antibodies are not specific and are cross-reactive with two closely related and ubiquitous bacteria, Escherichia coli and Citrobacter koseri. Our study describes the anti-Salmonella immune responses in tuatara and will help to inform decisions around maintaining wildlife health, as well as providing important insights into the role and development of adaptive immunity in reptilian species.
Collapse
Affiliation(s)
- Danielle M R L Middleton
- Allan Wilson Centre for Molecular Ecology and Evolution, Victoria University of Wellington, P.O. Box 600, Wellington, New Zealand.
| | - Nicola J Nelson
- Allan Wilson Centre for Molecular Ecology and Evolution, Victoria University of Wellington, P.O. Box 600, Wellington, New Zealand
| | - Brett D Gartrell
- Wildbase, Institute of Veterinary, Animal and Biomedical Science, Massey University, Private Bag 11-222, Palmerston North, New Zealand
| | - Anne C La Flamme
- Allan Wilson Centre for Molecular Ecology and Evolution, Victoria University of Wellington, P.O. Box 600, Wellington, New Zealand
| |
Collapse
|
37
|
Zhao P, Guo Y, Ma B, Xing M, Wang J. Generation and characterization of polyclonal antibody against part of immunoglobulin constant heavy υ chain of goose. Monoclon Antib Immunodiagn Immunother 2015; 33:287-90. [PMID: 25171010 DOI: 10.1089/mab.2013.0092] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Immunoglobulin Y (abbreviated as IgY) is a type of immunoglobulin that is the major antibody in bird, reptile, and lungfish blood. IgY consists of two light (λ) and two heavy (υ) chains. In the present study, polyclonal antibody against IgYFc was generated and evaluated. rIgYCυ3/Cυ4 was expressed in Escherichia coli, purified and utilized to raise polyclonal antibody in rabbit. High affinity antisera were obtained, which successfully detected the antigen at a dilution of 1:204,800 for ELISA assay. The antibody can specifically recognize both rIgYCυ3/Cυ4 and native IgY by Western bolt analysis. Furthermore, the serum of Grus japonensis or immunoglobulin of chicken, duck, turkey, and silkie samples and dynamic changes of serum GoIgY after immunogenicity with GPV-VP3-virus-like particles (GPV-VP3-VLPs) can be detected with the anti-GoIgYFc polyclonal antibody. These results suggested that the antibody is valuable for the investigation of biochemical properties and biological functions of GoIgY.
Collapse
Affiliation(s)
- Panpan Zhao
- 1 College of Wildlife Resources, Northeast Forestry University , Harbin, China
| | | | | | | | | |
Collapse
|
38
|
Abstract
Jawless vertebrates represented by lampreys and hagfish mount antigen-specific immune responses using variable lymphocyte receptors. These receptors generate diversity comparable to that of T-cell and B-cell receptors by assembling multiple leucine-rich repeat modules with highly variable sequences. Although it is true that jawed and jawless vertebrates have structurally unrelated antigen receptors, their adaptive immune systems have much in common. Most notable is the conservation of lymphocyte lineages. It appears that specialized lymphocyte lineages emerged in a common vertebrate ancestor and that jawed and jawless vertebrates co-opted different antigen receptors within the context of such lymphocyte lineages.
Collapse
Affiliation(s)
- Masanori Kasahara
- Department of Pathology, Hokkaido University Graduate School of Medicine, North 15 West 7, Sapporo, 060-8638, Japan.
| |
Collapse
|
39
|
Abstract
As in mammals, cartilaginous and teleost fishes possess adaptive immune systems based on antigen recognition by immunoglobulins (Ig), T cell receptors (TCR), and major histocompatibility complex molecules (MHC) I and MHC II molecules. Also it is well established that fish B cells and mammalian B cells share many similarities, including Ig gene rearrangements, and production of membrane Ig and secreted Ig forms. This chapter provides an overview of the IgH and IgL chains in cartilaginous and bony fish, including their gene organizations, expression, diversity of their isotypes, and development of the primary repertoire. Furthermore, when possible, we have included summaries of key studies on immune mechanisms such as allelic exclusion, somatic hypermutation, affinity maturation, class switching, and mucosal immune responses.
Collapse
Affiliation(s)
- Eva Bengtén
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, 39216-4505, USA.
| | - Melanie Wilson
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, 39216-4505, USA.
| |
Collapse
|
40
|
Abstract
Cells acquire their ultimate identities by activating combinations of transcription factors that initiate and sustain expression of the appropriate cell type-specific genes. T cell development depends on the progression of progenitor cells through three major phases, each of which is associated with distinct transcription factor ensembles that control the recruitment of these cells to the thymus, their proliferation, lineage commitment and responsiveness to T cell receptor signals, all before the allocation of cells to particular effector programmes. All three phases are essential for proper T cell development, as are the mechanisms that determine the boundaries between each phase. Cells that fail to shut off one set of regulators before the next gene network phase is activated are predisposed to leukaemic transformation.
Collapse
|
41
|
He L, Cao G, Huang M, Xue R, Hu X, Gong C. Expression pattern of immunoglobulin superfamily members in the silkworm, Bombyx mori. Gene 2014; 548:198-209. [PMID: 25020261 DOI: 10.1016/j.gene.2014.07.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 07/09/2014] [Accepted: 07/11/2014] [Indexed: 12/18/2022]
Abstract
Immunoglobulin superfamily (IgSF) proteins are involved in cell adhesion, cell communication and immune functions. In this study, 152 IgSF genes containing at least one immunoglobulin (Ig) domain were predicted in the Bombyx mori silkworm genome. Of these, 145 were distributed on 25 chromosomes with no genes on chromosomes 16, 18 and 26. Multiple sequence alignments and phylogenetic evolution analysis indicated that IgSFs evolved rapidly. Gene ontology (GO) annotation indicated that IgSF members functioned as cellular components and in molecular functions and biological processes. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis suggested that IgSF proteins were involved in signal transduction, signaling molecules and interaction, and cell communication. Microarray-based expression data showed tissue expression for 136 genes in anterior silkgland, middle silkgland, posterior silkgland, testis, ovary, fat body, midgut, integument, hemocyte, malpighian tubule and head. Expression pattern of IgSF genes in the silkworm ovary and midgut was analyzed by RNA-Seq. Expression of 105 genes was detected in the ovary in strain Dazao. Expression in the midgut was detected for 74 genes in strain Lan5 and 75 genes in strain Ou17. Expression of 34 IgSF genes in the midgut relative to the actin A3 gene was significantly different between strains Lan5 and Ou17. Furthermore, 1 IgSF gene was upregulated and 1 IgSF gene was downregulated in strain Lan5, and 4 IgSF genes were upregulated and 2 IgSF genes were downregulated in strain Ou17 after silkworms were challenged with B. mori cypovirus (BmCPV), indicating potential involvement in the response to BmCPV-infection. These results provide an overview of IgSF family members in silkworms, and lay the foundation for further functional studies.
Collapse
Affiliation(s)
- Lei He
- School of Biology & Basic Medical Science, Soochow University, Suzhou 215123, China
| | - Guangli Cao
- School of Biology & Basic Medical Science, Soochow University, Suzhou 215123, China; National Engineering Laboratory for Modern Silk, Soochow University, Suzhou, China
| | - Moli Huang
- School of Biology & Basic Medical Science, Soochow University, Suzhou 215123, China
| | - Renyu Xue
- School of Biology & Basic Medical Science, Soochow University, Suzhou 215123, China; National Engineering Laboratory for Modern Silk, Soochow University, Suzhou, China
| | - Xiaolong Hu
- School of Biology & Basic Medical Science, Soochow University, Suzhou 215123, China; National Engineering Laboratory for Modern Silk, Soochow University, Suzhou, China
| | - Chengliang Gong
- School of Biology & Basic Medical Science, Soochow University, Suzhou 215123, China; National Engineering Laboratory for Modern Silk, Soochow University, Suzhou, China.
| |
Collapse
|
42
|
Krishnaswamy Gopalan T, Gururaj P, Gupta R, Gopal DR, Rajesh P, Chidambaram B, Kalyanasundaram A, Angamuthu R. Transcriptome profiling reveals higher vertebrate orthologous of intra-cytoplasmic pattern recognition receptors in grey bamboo shark. PLoS One 2014; 9:e100018. [PMID: 24956167 PMCID: PMC4067322 DOI: 10.1371/journal.pone.0100018] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 05/21/2014] [Indexed: 01/31/2023] Open
Abstract
From an immunologist perspective, sharks are an important group of jawed cartilaginous fishes and survey of the public database revealed a great gap in availability of large-scale sequence data for the group of Chondrichthyans the elasmobranchs. In an attempt to bridge this deficit we generated the transcriptome from the spleen and kidney tissues (a total of 1,606,172 transcripts) of the shark, Chiloscyllium griseum using the Illumina HiSeq2000 platform. With a cut off of > = 300 bp and an expression value of >1RPKM we used 43,385 transcripts for BLASTX analysis which revealed 17,548 transcripts matching to the NCBI nr database with an E-value of < = 10(-5) and similarity score of 40%. The longest transcript was 16,974 bases with matched to HECT domain containing E3 ubiqutin protein ligase. MEGAN4 annotation pipeline revealed immune and signalling pathways including cell adhesion molecules, cytokine-cytokine receptor interaction, T-cell receptor signalling pathway and chemokine signaling pathway to be highly expressed in spleen, while different metabolism pathways such as amino acid metabolism, carbohydrate metabolism, lipid metabolism and xenobiotic biodegradation were highly expressed in kidney. Few of the candidate genes were selected to analyze their expression levels in various tissues by real-time PCR and also localization of a receptor by in-situ PCR to validate the prediction. We also predicted the domains structures of some of the identified pattern recognition receptors, their phylogenetic relationship with lower and higher vertebrates and the complete downstream signaling mediators of classical dsRNA signaling pathway. The generated transcriptome will be a valuable resource to further genetic and genomic research in elasmobranchs.
Collapse
Affiliation(s)
- Tirumurugaan Krishnaswamy Gopalan
- Department of Animal Biotechnology and Translational Research Platform for Veterinary Biologicals, Tamil Nadu Veterinary and Animal Sciences University, Chennai, Tamil Nadu, India
| | - Pradheepa Gururaj
- Department of Animal Biotechnology, Tamil Nadu Veterinary and Animal Sciences University, Chennai, Tamil Nadu, India
| | - Ravi Gupta
- SciGenom Labs Pvt. Ltd., Kakkanad, Cochin, Kerala, India
| | - Dhinakar Raj Gopal
- Department of Animal Biotechnology and Translational Research Platform for Veterinary Biologicals, Tamil Nadu Veterinary and Animal Sciences University, Chennai, Tamil Nadu, India
| | - Preeti Rajesh
- SciGenom Labs Pvt. Ltd., Kakkanad, Cochin, Kerala, India
| | - Balachandran Chidambaram
- Department of Veterinary Pathology, Tamil Nadu Veterinary and Animal Sciences University, Chennai, Tamil Nadu, India
| | - Aravindan Kalyanasundaram
- Department of Animal Biotechnology, Tamil Nadu Veterinary and Animal Sciences University, Chennai, Tamil Nadu, India
| | - Raja Angamuthu
- Department of Animal Biotechnology, Tamil Nadu Veterinary and Animal Sciences University, Chennai, Tamil Nadu, India
| |
Collapse
|
43
|
Zhu L, Yan Z, Feng M, Peng D, Guo Y, Hu X, Ren L, Sun Y. Identification of sturgeon IgD bridges the evolutionary gap between elasmobranchs and teleosts. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2014; 42:138-147. [PMID: 24001581 DOI: 10.1016/j.dci.2013.08.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 08/22/2013] [Accepted: 08/24/2013] [Indexed: 06/02/2023]
Abstract
IgD has been found in almost all jawed vertebrates, including cartilaginous and teleost fish. However, IgD is missing in acipenseriformes, a branch that is evolutionarily positioned between elasmobranchs and teleost fish. Here, by analyzing transcriptome data, we identified a transcriptionally active IgD-encoding gene in the Siberian sturgeon (Acipenser baerii). Phylogenetic analysis indicated that it is orthologous to mammalian IgD and closely related to the IgD of other fish. The lengths of sturgeon membrane-bound IgD transcripts ranged from 1.2kb to 6.2kb, encoding 3-19 CH domains. As in teleosts, the first CH domain of the sturgeon IgD transcript is also derived from μCH1 by RNA splicing. However, the variable region of the expressed sturgeon IgD shows limited V(D)J usage. In addition to IgD, three IgM variants were also identified in this species, whereas no IgT/Z-encoding genes were observed. This study bridges the gap in Ig evolution between elasmobranchs and teleosts and provides significant insight into the early evolution of immunoglobulins.
Collapse
Affiliation(s)
- Lin Zhu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, PR China
| | | | | | | | | | | | | | | |
Collapse
|
44
|
Sharon G, Pimenta Leibowitz M, Chettri JK, Isakov N, Zilberg D. Comparative Study of Infection with Tetrahymena of Different Ornamental Fish Species. J Comp Pathol 2014; 150:316-24. [DOI: 10.1016/j.jcpa.2013.08.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 07/11/2013] [Accepted: 08/28/2013] [Indexed: 10/26/2022]
|
45
|
Scapigliati G. Functional aspects of fish lymphocytes. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2013; 41:200-208. [PMID: 23707785 DOI: 10.1016/j.dci.2013.05.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Revised: 05/15/2013] [Accepted: 05/15/2013] [Indexed: 06/02/2023]
Abstract
After almost 40 years of studies in comparative immunology, some light has been shed on the evolutive immunobiology of vertebrates, and experimental evidences have shown that acquired immunity, defined by somatic recombination of antigen-binding molecules and memory, is an achievement as ancient as jawless vertebrates. However, the molecular processes generating antigen receptors evolved independently between jawless and jawed fishes, and produced lymphocytic cells with similar functions but employing different sets of genes. In recent years, data have been provided describing some in vitro and in vivo functional responses of fish lymphocytes. After a long gap, the number of specific markers for fish lymphocytes is increasing, thus allowing a first characterisation of lymphocyte subsets. Overall, in the near future it will be possible to open a new chapter in fish immunology and investigate functional immunity of lymphocyte responses by combining the extensive knowledge on immune gene products with markers for molecules and cells. The present review summarizes current knowledge on functional features of fish lymphocytes.
Collapse
Affiliation(s)
- Giuseppe Scapigliati
- Department for Innovation in Biological, Agro-food and Forest Systems, University of Tuscia, Largo dell'Università, 01100 Viterbo, Italy.
| |
Collapse
|
46
|
Abstract
Jawless vertebrates (cyclostomes) have an alternative adaptive immune system in which lymphocytes somatically diversify their variable lymphocyte receptors (VLR) through recombinatorial use of leucine-rich repeat cassettes during VLR gene assembly. Three types of these anticipatory receptors in lampreys (VLRA, VLRB, and VLRC) are expressed by separate lymphocyte lineages. However, only two VLR genes (VLRA and VLRB) have been found in hagfish. Here we have identified a third hagfish VLR, which undergoes somatic assembly to generate sufficient diversity to encode a large repertoire of anticipatory receptors. Sequence analysis, structural comparison, and phylogenetic analysis indicate that the unique hagfish VLR is the counterpart of lamprey VLRA and the previously identified hagfish "VLRA" is the lamprey VLRC counterpart. The demonstration of three orthologous VLR genes in both lampreys and hagfish suggests that this anticipatory receptor system evolved in a common ancestor of the two cyclostome lineages around 480 Mya.
Collapse
|
47
|
Epigonal conditioned media from bonnethead shark, Sphyrna tiburo, induces apoptosis in a T-cell leukemia cell line, Jurkat E6-1. Mar Drugs 2013; 11:3224-57. [PMID: 24065163 PMCID: PMC3806469 DOI: 10.3390/md11093224] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 08/12/2013] [Accepted: 08/20/2013] [Indexed: 12/17/2022] Open
Abstract
Representatives of Subclass Elasmobranchii are cartilaginous fish whose members include sharks, skates, and rays. Because of their unique phylogenetic position of being the most primitive group of vertebrates to possess all the components necessary for an adaptive immune system, the immune regulatory compounds they possess may represent the earliest evolutionary forms of novel compounds with the potential for innovative therapeutic applications. Conditioned medium, generated from short term culture of cells from the epigonal organ of bonnethead sharks (Sphyrna tiburo), has been shown to have potent reproducible cytotoxic activity against a variety of human tumor cell lines in vitro. Existing data suggest that epigonal conditioned medium (ECM) exerts this cytotoxic activity through induction of apoptosis in target cells. This manuscript describes apoptosis induction in a representative tumor cell line, Jurkat E6-1, in response to treatment with ECM at concentrations of 1 and 2 mg/mL. Data indicate that ECM exposure initiates the mitochondrial pathway of apoptosis through activation of caspase enzymes. Future purification of ECM components may result in the isolation of an immune-regulatory compound with potential therapeutic benefit for treatment of human cancer.
Collapse
|
48
|
Zhang C, Du Pasquier L, Hsu E. Shark IgW C region diversification through RNA processing and isotype switching. THE JOURNAL OF IMMUNOLOGY 2013; 191:3410-8. [PMID: 23935192 DOI: 10.4049/jimmunol.1301257] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Sharks and skates represent the earliest vertebrates with an adaptive immune system based on lymphocyte Ag receptors generated by V(D)J recombination. Shark B cells express two classical Igs, IgM and IgW, encoded by an early, alternative gene organization consisting of numerous autonomous miniloci, where the individual gene cluster carries a few rearranging gene segments and one C region, μ or ω. We have characterized eight distinct Ig miniloci encoding the nurse shark ω H chain. Each cluster consists of VH, D, and JH segments and six to eight C domain exons. Two interspersed secretory exons, in addition to the 3'-most C exon with tailpiece, provide the gene cluster with the ability to generate at least six secreted isoforms that differ as to polypeptide length and C domain combination. All clusters appear to be functional, as judged by the capability for rearrangement and absence of defects in the deduced amino acid sequence. We previously showed that IgW VDJ can perform isotype switching to μ C regions; in this study, we found that switching also occurs between ω clusters. Thus, C region diversification for any IgW VDJ can take place at the DNA level by switching to other ω or μ C regions, as well as by RNA processing to generate different C isoforms. The wide array of pathogens recognized by Abs requires different disposal pathways, and our findings demonstrate complex and unique pathways for C effector function diversity that evolved independently in cartilaginous fishes.
Collapse
Affiliation(s)
- Cecilia Zhang
- Department of Physiology and Pharmacology, State University of New York Health Science Center at Brooklyn, Brooklyn, NY 11203, USA
| | | | | |
Collapse
|
49
|
Extensive diversification of IgH subclass-encoding genes and IgM subclass switching in crocodilians. Nat Commun 2013; 4:1337. [PMID: 23299887 DOI: 10.1038/ncomms2317] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 11/22/2012] [Indexed: 01/01/2023] Open
Abstract
Crocodilians are a group of reptiles that are closely related to birds and are thought to possess a strong immune system. Here we report that the IgH locus in the Siamese crocodile and the Chinese alligator contains multiple μ genes, in contrast to other tetrapods. Both the μ2 and μ3 genes are expressed through class-switch recombination involving the switch region and germline transcription. Both IgM1 and IgM2 are present in the serum as polymers, which implies that IgM class switching may have significant roles in humoural immunity. The crocodilian α genes are the first IgA-encoding genes identified in reptiles, and these genes show an inverted transcriptional orientation similar to that of birds. The identification of both α and δ genes in crocodilians suggests that the IgH loci of modern living mammals, reptiles and birds share a common ancestral organization.
Collapse
|
50
|
Organization of lamprey variable lymphocyte receptor C locus and repertoire development. Proc Natl Acad Sci U S A 2013; 110:6043-8. [PMID: 23487799 DOI: 10.1073/pnas.1302500110] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Jawless vertebrates are pivotal representatives for studies of the evolution of adaptive immunity due to their unique position in chordate phylogeny. Lamprey and hagfish, the extant jawless vertebrates, have an alternative lymphocyte-based adaptive immune system that is based on somatically diversifying leucine-rich repeat (LRR)-based antigen receptors, termed variable lymphocyte receptors (VLRs). Lamprey T-like and B-like lymphocyte lineages have been shown to express VLRA and VLRB types of anticipatory receptors, respectively. An additional VLR type, termed VLRC, has recently been identified in arctic lamprey (Lethenteron camtschaticum), and our analysis indicates that VLRC sequences are well conserved in sea lamprey (Petromyzon marinus), L. camtschaticum, and European brook lamprey (Lampetra planeri). Genome sequences of P. marinus were analyzed to determine the organization of the VLRC-encoding locus. In addition to the incomplete germ-line VLRC gene, we have identified 182 flanking donor genomic sequences that could be used to complete the assembly of mature VLRC genes. Donor LRR cassettes were classifiable into five basic structural groups, the composition of which determines their order of use during VLRC assembly by virtue of sequence similarities to the incomplete germ-line gene and to one another. Bidirectional VLRC assembly was predicted by comparisons of mature VLRC genes with the sequences of donor LRR cassettes and verified by analysis of partially assembled intermediates. Biased and repetitive use of certain donor LRR cassettes was demonstrable in mature VLRCs. Our analysis provides insight into the unique molecular strategies used for VLRC gene assembly and repertoire diversification.
Collapse
|