1
|
Lim SJ, Jithpratuck W, Wasylik K, Sriaroon P, Dishaw LJ. Associations of Microbial Diversity with Age and Other Clinical Variables among Pediatric Chronic Rhinosinusitis (CRS) Patients. Microorganisms 2023; 11:microorganisms11020422. [PMID: 36838387 PMCID: PMC9965780 DOI: 10.3390/microorganisms11020422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/24/2023] [Accepted: 02/02/2023] [Indexed: 02/11/2023] Open
Abstract
Chronic rhinosinusitis (CRS) is a heterogenous disease that causes persistent paranasal sinus inflammation in children. Microorganisms are thought to contribute to the etiology and progression of CRS. Culture-independent microbiome analysis offers deeper insights into sinonasal microbial diversity and microbe-disease associations than culture-based methods. To date, CRS-related microbiome studies have mostly focused on the adult population, and only one study has characterized the pediatric CRS microbiome. In this study, we analyzed the bacterial diversity of adenoid tissue, adenoid swab, maxillary sinus, and sinus wash samples from 45 pediatric CRS patients recruited from the Johns Hopkins All Children's Hospital (JHACH) in St. Petersburg, FL, USA. The alpha diversity in these samples was associated with baseline nasal steroid use, leukotriene receptor antagonist (LTRA) use, and total serum immunoglobulin (Ig) E (IgE) level. Streptococcus, Moraxella, and Haemophilus spp. were most frequently identified from sinus cultures and the sequenced 16S rRNA gene content. Comparative analyses combining our samples with the samples from the previous microbiome study revealed differentially abundant genera between patients with pediatric CRS and healthy controls, including Cutibacterium and Moraxella. Additionally, the abundances of Streptobacillus and Staphylococcus were consistently correlated with age in both adenoid- and sinus-derived samples. Our study uncovers new associations of alpha diversity with clinical parameters, as well as associations of specific genera with disease status and age, that can be further investigated.
Collapse
Affiliation(s)
- Shen Jean Lim
- Department of Pediatrics, Morsani College of Medicine, University of South Florida, Tampa, FL 33620, USA
| | - Warit Jithpratuck
- Department of Pediatrics, Morsani College of Medicine, University of South Florida, Tampa, FL 33620, USA
| | - Kathleen Wasylik
- Pediatric Ear, Nose & Throat Specialists, Johns Hopkins All Children’s Hospital, St. Petersburg, FL 33701, USA
| | - Panida Sriaroon
- Department of Pediatrics, Morsani College of Medicine, University of South Florida, Tampa, FL 33620, USA
- USF Pediatric Allergy/Immunology Clinic, Food Allergy Clinic, Johns Hopkins All Children’s Hospital, St. Petersburg, FL 33701, USA
| | - Larry J. Dishaw
- Department of Pediatrics, Morsani College of Medicine, University of South Florida, Tampa, FL 33620, USA
- Correspondence: ; Tel.: +1-727-553-3601
| |
Collapse
|
2
|
Liberti A, Natarajan O, Atkinson CGF, Dishaw LJ. Secreted immunoglobulin domain effector molecules of invertebrates and management of gut microbial ecology. Immunogenetics 2022; 74:99-109. [PMID: 34988622 DOI: 10.1007/s00251-021-01237-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 11/18/2021] [Indexed: 02/01/2023]
Abstract
The origins of a "pass-through" gut in early bilaterians facilitated the exploration of new habitats, motivated the innovation of feeding styles and behaviors, and helped drive the evolution of more complex organisms. The gastrointestinal tract has evolved to consist of a series of interwoven exchanges between nutrients, host immunity, and an often microbe-rich environmental interface. Not surprisingly, animals have expanded their immune repertoires to include soluble effectors that can be secreted into luminal spaces, e.g., in the gut, facilitating interactions with microbes in ways that influence their settlement dynamics, virulence, and their interaction with other microbes. The immunoglobulin (Ig) domain, which is also found in some non-immune molecules, is recognized as one of the most versatile recognition domains lying at the interface of innate and adaptive immunity; among vertebrates, secreted Igs are known to play crucial roles in the management of gut microbial communities. In this mini-review, we will focus on secreted immune effectors possessing Ig-like domains in invertebrates, such as the fibrinogen-related effector proteins first described in the gastropod Biomphalaria glabrata, the Down syndrome cellular adhesion molecule first described in the arthropod, Drosophila melanogaster, and the variable region-containing chitin-binding proteins of the protochordates. We will highlight our current understanding of their function and their potential role, if not yet recognized, in the establishment and maintenance of host-microbial interfaces and argue that these Igs are likely also essential to microbiome management.
Collapse
Affiliation(s)
- Assunta Liberti
- Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Ojas Natarajan
- Department of Pediatrics, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.,Division of Molecular Genetics, Children's Research Institute, St. Petersburg, FL, USA
| | - Celine Grace F Atkinson
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL, USA.,Division of Molecular Genetics, Children's Research Institute, St. Petersburg, FL, USA
| | - Larry J Dishaw
- Department of Pediatrics, Morsani College of Medicine, University of South Florida, Tampa, FL, USA. .,Division of Molecular Genetics, Children's Research Institute, St. Petersburg, FL, USA.
| |
Collapse
|
3
|
Liberti A, Leigh BA, Graham Z, Natarajan O, Dishaw LJ. A Role for Secreted Immune Effectors in Microbial Biofilm Formation Revealed by Simple In Vitro Assays. Methods Mol Biol 2022; 2421:127-140. [PMID: 34870816 DOI: 10.1007/978-1-0716-1944-5_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The formation of biofilms is critical for the successful and stable colonization of mucosal surfaces by microbes, which often build three-dimensional environments by exuding exopolysaccharides and other macromolecules such as proteins, lipids, and even DNA. It is not just bacteria, but fungi such as yeast, that form these adherent interacting communities. Historically, biofilms have been studied in the context of pathogenesis, but only recently it has been recognized that important relationships among members of host-associated microbiomes are maintained within the context of biofilms. Host immune responses impact biofilm formation in various ways; for example, it is likely that formation of stable biofilms by non-pathogens improves barrier defenses by not just filling available niche spaces but also by helping to ward off pathogens directly. Recently, it was found that soluble immune effector molecules such as immunoglobulin A (IgA) in mammals serve essential roles in modulating complex biofilm communities in ways that benefit the host. Additional lines of evidence from other secreted immune effectors, such as the variable region-containing chitin-binding proteins (VCBPs) in protochordates, now suggest that this phenomenon is much more widespread than previously recognized. The activity of these immune molecules also likely serves roles beyond those of simple defense strategies; rather, they may be improving the outcome of symbiotic interactions benefiting the host. Thus, traditional immune assays that are aimed at studying the function of secreted immune effectors, such as agglutination assays, should take into account the possibility that the first observation may not be the last if the microbes under study are not directly killed. Here, we describe a series of simple approaches to characterize biofilm formation when bacteria (or yeast) are cultured in the presence of a secreted immune effector. To model this approach, we use microbes isolated from the gut of Ciona robusta, each grown in the presence or absence of VCBPs. The approaches defined here are amenable to diverse model systems and their microbes.
Collapse
Affiliation(s)
- Assunta Liberti
- Department of Pediatrics, Morsani College of Medicine, Children's Research Institute, University of South Florida, Saint Petersburg, FL, USA
- Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Brittany A Leigh
- Department of Pediatrics, Morsani College of Medicine, Children's Research Institute, University of South Florida, Saint Petersburg, FL, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Zachary Graham
- Department of Pediatrics, Morsani College of Medicine, Children's Research Institute, University of South Florida, Saint Petersburg, FL, USA
| | - Ojas Natarajan
- Department of Pediatrics, Morsani College of Medicine, Children's Research Institute, University of South Florida, Saint Petersburg, FL, USA
| | - Larry J Dishaw
- Department of Pediatrics, Morsani College of Medicine, Children's Research Institute, University of South Florida, Saint Petersburg, FL, USA.
| |
Collapse
|
4
|
Liberti A, Natarajan O, Atkinson CGF, Sordino P, Dishaw LJ. Reflections on the Use of an Invertebrate Chordate Model System for Studies of Gut Microbial Immune Interactions. Front Immunol 2021; 12:642687. [PMID: 33717199 PMCID: PMC7947342 DOI: 10.3389/fimmu.2021.642687] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 01/20/2021] [Indexed: 12/11/2022] Open
Abstract
The functional ecology of the gastrointestinal tract impacts host physiology, and its dysregulation is at the center of various diseases. The immune system, and specifically innate immunity, plays a fundamental role in modulating the interface of host and microbes in the gut. While humans remain a primary focus of research in this field, the use of diverse model systems help inform us of the fundamental principles legislating homeostasis in the gut. Invertebrates, which lack vertebrate-style adaptive immunity, can help define conserved features of innate immunity that shape the gut ecosystem. In this context, we previously proposed the use of a marine invertebrate, the protochordate Ciona robusta, as a novel tractable model system for studies of host-microbiome interactions. Significant progress, reviewed herein, has been made to fulfill that vision. We examine and review discoveries from Ciona that include roles for a secreted immune effector interacting with elements of the microbiota, as well as chitin-rich mucus lining the gut epithelium, the gut-associated microbiome of adults, and the establishment of a large catalog of cultured isolates with which juveniles can be colonized. Also discussed is the establishment of methods to rear the animals germ-free, an essential technology for dissecting the symbiotic interactions at play. As the foundation is now set to extend these studies into the future, broadening our comprehension of how host effectors shape the ecology of these microbial communities in ways that establish and maintain homeostasis will require full utilization of "multi-omics" approaches to merge computational sciences, modeling, and experimental biology in hypothesis-driven investigations.
Collapse
Affiliation(s)
- Assunta Liberti
- Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Ojas Natarajan
- Morsani College of Medicine, Department of Pediatrics, University of South Florida, Tampa, FL, United States
- Division of Molecular Genetics, Children’s Research Institute, St. Petersburg, FL, United States
| | - Celine Grace F. Atkinson
- Division of Molecular Genetics, Children’s Research Institute, St. Petersburg, FL, United States
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL, United States
| | - Paolo Sordino
- Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Larry J. Dishaw
- Morsani College of Medicine, Department of Pediatrics, University of South Florida, Tampa, FL, United States
- Division of Molecular Genetics, Children’s Research Institute, St. Petersburg, FL, United States
| |
Collapse
|
5
|
Groer MW, Miller EM, D'Agata A, Ho TTB, Dutra SV, Yoo JY, Yee AL, Gilbert JA, Dishaw LJ. Contributors to Dysbiosis in Very-Low-Birth-Weight Infants. J Obstet Gynecol Neonatal Nurs 2020; 49:232-242. [PMID: 32247727 DOI: 10.1016/j.jogn.2020.02.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2020] [Indexed: 02/08/2023] Open
Abstract
The objective of this commentary was to analyze the causes and outcomes of gut microbiome dysbiosis in preterm infants who are born at very low birth weight (VLBW). The intrauterine development of VLBW infants is interrupted abruptly with preterm birth and followed by extrauterine, health-threatening conditions and sequelae. These infants develop intestinal microbial dysbiosis characterized by low diversity, an overall reduction in beneficial and/or commensal bacteria, and enrichment of opportunistic pathogens of the Gammaproteobacteria class. The origin of VLBW infant dysbiosis is not well understood and is likely the result of a combination of immaturity and medical care. We propose that these factors interact to produce inflammation in the gut, which further perpetuates dysbiosis. Understanding the sources of dysbiosis could result in interventions to reduce gut inflammation, decrease enteric pathology, and improve health outcomes for these vulnerable infants.
Collapse
|
6
|
Liberti A, Cannon JP, Litman GW, Dishaw LJ. A Soluble Immune Effector Binds Both Fungi and Bacteria via Separate Functional Domains. Front Immunol 2019; 10:369. [PMID: 30894858 PMCID: PMC6414549 DOI: 10.3389/fimmu.2019.00369] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 02/13/2019] [Indexed: 12/21/2022] Open
Abstract
The gut microbiome of animals consists of diverse microorganisms that include both prokaryotes and eukaryotes. Complex interactions occur among these inhabitants, as well as with the immune system of the host, and profoundly influence the overall health of both the host and its microbial symbionts. Despite the enormous importance for the host to regulate its gut microbiome, the extent to which animals generate immune-related molecules with the capacity to directly influence polymicrobial interactions remains unclear. The urochordate, Ciona robusta, is a model organism that has been adapted to experimental studies of host/microbiome interactions. Ciona variable-region containing chitin-binding proteins (VCBPs) are innate immune effectors, composed of immunoglobulin (Ig) variable regions and a chitin-binding domain (CBD) and are expressed in high abundance in the gut. It was previously shown that VCBP-C binds bacteria and influences both phagocytosis by granular amoebocytes and biofilm formation via its Ig domains. We show here that the CBD of VCBP-C independently recognizes chitin molecules present in the cell walls, sporangia (spore-forming bodies), and spores of a diverse set of filamentous fungi isolated from the gut of Ciona. To our knowledge, this is the first description of a secreted Ig-containing immune molecule with the capacity to directly promote transkingdom interactions through simultaneous binding by independent structural domains and could have broad implications in modulating the establishment, succession, and homeostasis of gut microbiomes.
Collapse
Affiliation(s)
- Assunta Liberti
- Department of Pediatrics, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
| | - John P. Cannon
- Department of Pediatrics, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
| | - Gary W. Litman
- Department of Pediatrics, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
- Department of Molecular Genetics, Children's Research Institute, Johns Hopkins All Children's Hospital, St. Petersburg, FL, United States
| | - Larry J. Dishaw
- Department of Pediatrics, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
| |
Collapse
|
7
|
Yee AL, Miller E, Dishaw LJ, Gordon JM, Ji M, Dutra S, Ho TTB, Gilbert JA, Groer M. Longitudinal Microbiome Composition and Stability Correlate with Increased Weight and Length of Very-Low-Birth-Weight Infants. mSystems 2019; 4:e00229-18. [PMID: 30834328 PMCID: PMC6392092 DOI: 10.1128/msystems.00229-18] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 01/18/2019] [Indexed: 01/01/2023] Open
Abstract
The microbiomes of 83 preterm very-low-birth-weight (VLBW) infants and clinical covariates were analyzed weekly over the course of their initial neonatal intensive care unit (NICU) stay, with infant growth as the primary clinical outcome. Birth weight significantly correlated with increased rate of weight gain in the first 6 weeks of life, while no significant relationship was observed between rate of weight gain and feeding type. Microbial diversity increased with age and was significantly correlated with weight gain and percentage of the mother's own milk. As expected, infants who received antibiotics during their NICU stay had significantly lower alpha diversity than those who did not. Of those in the cohort, 25 were followed into childhood. Alpha diversity significantly increased between NICU discharge and age 2 years and between age 2 years and age 4 years, but the microbial alpha diversity of 4-year-old children was not significantly different from that of mothers. Infants who showed improved length over the course of their NICU stay had significantly more volatile microbial beta diversity results than and a significantly decreased microbial maturity index compared with infants who did not; interestingly, all infants who showed improved length during the NICU stay were delivered by Caesarean section. Microbial beta diversity results were significantly different between the time of the NICU stay and all other time points (for children who were 2 or 4 years old and mothers when their children were 2 or 4 years old). IMPORTANCE Preterm infants are at greater risk of microbial insult than full-term infants, including reduced exposure to maternal vaginal and enteric microbes, higher rates of formula feeding, invasive procedures, and administration of antibiotics and medications that alter gastrointestinal pH. This investigation of the VLBW infant microbiome over the course of the neonatal intensive care unit (NICU) stay, and at ages 2 and 4 years, showed that the only clinical variables associated with significant differences in taxon abundance were weight gain during NICU stay (Klebsiella and Staphylococcus) and antibiotic administration (Streptococcus and Bifidobacterium). At 2 and 4 years of age, the microbiota of these VLBW infants became similar to the mothers' microbiota. The number of microbial taxa shared between the infant or toddler and the mother varied, with least the overlap between infants and mothers. Overall, there was a significant association between the diversity and structure of the microbial community and infant weight and length gain in an at-risk childhood population.
Collapse
Affiliation(s)
- Alyson L. Yee
- Interdisciplinary Scientist Training Program, University of Chicago, Chicago, Illinois, USA
- Microbiome Center, University of Chicago, Chicago, Illinois, USA
| | - Elizabeth Miller
- Department of Anthropology, College of Arts and Sciences, University of South Florida, Tampa, Florida, USA
| | - Larry J. Dishaw
- Department of Pediatrics, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Jessica M. Gordon
- College of Nursing, University of South Florida, Tampa, Florida, USA
| | - Ming Ji
- College of Nursing, University of South Florida, Tampa, Florida, USA
| | - Samia Dutra
- College of Nursing, University of South Florida, Tampa, Florida, USA
| | - Thao T. B. Ho
- Department of Pediatrics, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Jack A. Gilbert
- Microbiome Center, University of Chicago, Chicago, Illinois, USA
- Department of Surgery, University of Chicago, Chicago, Illinois, USA
- Argonne National Laboratory, Chicago, Illinois, USA
| | - Maureen Groer
- College of Nursing, University of South Florida, Tampa, Florida, USA
| |
Collapse
|
8
|
Creasy A, Rosario K, Leigh BA, Dishaw LJ, Breitbart M. Unprecedented Diversity of ssDNA Phages from the Family Microviridae Detected within the Gut of a Protochordate Model Organism ( Ciona robusta). Viruses 2018; 10:v10080404. [PMID: 30065169 PMCID: PMC6116155 DOI: 10.3390/v10080404] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 07/23/2018] [Accepted: 07/27/2018] [Indexed: 12/13/2022] Open
Abstract
Phages (viruses that infect bacteria) play important roles in the gut ecosystem through infection of bacterial hosts, yet the gut virome remains poorly characterized. Mammalian gut viromes are dominated by double-stranded DNA (dsDNA) phages belonging to the order Caudovirales and single-stranded DNA (ssDNA) phages belonging to the family Microviridae. Since the relative proportion of each of these phage groups appears to correlate with age and health status in humans, it is critical to understand both ssDNA and dsDNA phages in the gut. Building upon prior research describing dsDNA viruses in the gut of Ciona robusta, a marine invertebrate model system used to study gut microbial interactions, this study investigated ssDNA phages found in the Ciona gut. We identified 258 Microviridae genomes, which were dominated by novel members of the Gokushovirinae subfamily, but also represented several proposed phylogenetic groups (Alpavirinae, Aravirinae, Group D, Parabacteroides prophages, and Pequeñovirus) and a novel group. Comparative analyses between Ciona specimens with full and cleared guts, as well as the surrounding water, indicated that Ciona retains a distinct and highly diverse community of ssDNA phages. This study significantly expands the known diversity within the Microviridae family and demonstrates the promise of Ciona as a model system for investigating their role in animal health.
Collapse
Affiliation(s)
- Alexandria Creasy
- College of Marine Science, University of South Florida, St. Petersburg, FL 33701, USA.
- Department of Pediatrics, Children's Research Institute, University of South Florida, St. Petersburg, FL 33701, USA.
| | - Karyna Rosario
- College of Marine Science, University of South Florida, St. Petersburg, FL 33701, USA.
| | - Brittany A Leigh
- College of Marine Science, University of South Florida, St. Petersburg, FL 33701, USA.
- Department of Pediatrics, Children's Research Institute, University of South Florida, St. Petersburg, FL 33701, USA.
| | - Larry J Dishaw
- Department of Pediatrics, Children's Research Institute, University of South Florida, St. Petersburg, FL 33701, USA.
| | - Mya Breitbart
- College of Marine Science, University of South Florida, St. Petersburg, FL 33701, USA.
| |
Collapse
|
9
|
Liberti A, Zucchetti I, Melillo D, Skapura D, Shibata Y, De Santis R, Pinto MR, Litman GW, Dishaw LJ. Chitin protects the gut epithelial barrier in a protochordate model of DSS-induced colitis. Biol Open 2018; 7:bio.029355. [PMID: 29222175 PMCID: PMC5827265 DOI: 10.1242/bio.029355] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The gastrointestinal tract of Ciona intestinalis, a solitary tunicate that siphon-filters water, shares similarities with its mammalian counterpart. The Ciona gut exhibits other features that are unique to protochordates, including certain immune molecules, and other characteristics, e.g. chitin-rich mucus, which appears to be more widespread than considered previously. Exposure of Ciona to dextran sulphate sodium (DSS) induces a colitis-like phenotype similar to that seen in other systems, and is characterized by alteration of epithelial morphology and infiltration of blood cells into lamina propria-like regions. DSS treatment also influences the production and localization of a secreted immune molecule shown previously to co-localize to chitin-rich mucus in the gut. Resistance to DSS is enhanced by exposure to exogenous chitin microparticles, suggesting that endogenous chitin is critical to barrier integrity. Protochordates, such as Ciona, retain basic characteristics found in other more advanced chordates and can inform us of uniquely conserved signals shaping host-microbiota interactions in the absence of adaptive immunity. These simpler model systems may also reveal factors and processes that modulate recovery from colitis, the role gut microbiota play in the onset of the disease, and the rules that help govern the reestablishment and maintenance of gut homeostasis.
Collapse
Affiliation(s)
- Assunta Liberti
- Department of Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Napoli 80121, Italy .,University of South Florida, Morsani College of Medicine, Department of Pediatrics, Tampa, FL 33606, USA
| | - Ivana Zucchetti
- Department of Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Napoli 80121, Italy
| | - Daniela Melillo
- Department of Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Napoli 80121, Italy.,Institute of Protein Biochemistry (IBP), National Research Council (CNR), Napoli 80131, Italy
| | - Diana Skapura
- Molecular Genetics, Johns Hopkins All Children's Hospital, Saint Petersburg, FL 33701, USA
| | - Yoshimi Shibata
- Biomedical Science Department, Florida Atlantic University, Charles E. Schmidt College of Medicine, Boca Raton, FL 33431, USA
| | - Rosaria De Santis
- Department of Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Napoli 80121, Italy
| | - Maria Rosaria Pinto
- Department of Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Napoli 80121, Italy
| | - Gary W Litman
- University of South Florida, Morsani College of Medicine, Department of Pediatrics, Tampa, FL 33606, USA
| | - Larry J Dishaw
- University of South Florida, Morsani College of Medicine, Department of Pediatrics, Tampa, FL 33606, USA
| |
Collapse
|
10
|
Leigh BA, Djurhuus A, Breitbart M, Dishaw LJ. The gut virome of the protochordate model organism, Ciona intestinalis subtype A. Virus Res 2017; 244:137-146. [PMID: 29155033 DOI: 10.1016/j.virusres.2017.11.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 11/14/2017] [Accepted: 11/14/2017] [Indexed: 02/06/2023]
Abstract
The identification of host-specific bacterial and viral communities associated with diverse animals has led to the concept of the metaorganism, which defines the animal and all of its associated microbes as a single unit. Here we sequence the viruses found in the gut (i.e., the gut virome) of the marine invertebrate model system, Ciona intestinalis subtype A, in samples collected one year apart. We present evidence for a host-associated virome that is distinct from the surrounding seawater and contains some temporally-stable members. Comparison of gut tissues before and after starvation in virus-free water enabled the differentiation between the Ciona-specific virome and transient viral communities associated with dietary sources. The Ciona gut viromes were dominated by double-stranded DNA tailed phages (Order Caudovirales) and sequence assembly yielded a number of complete circular phage genomes, most of which were highly divergent from known genomes. Unique viral communities were found in distinct gut niches (stomach, midgut and hindgut), paralleling the compartmentalization of bacterial communities. Additionally, integrase and excisionase genes, including many that are similar to prophage sequences within the genomes of bacterial genera belonging to the Ciona core microbiome, were prevalent in the viromes, indicating the active induction of prophages within the gut ecosystem. Knowledge of the gut virome of this model organism lays the foundation for studying the interactions between viruses, bacteria, and host immunity.
Collapse
Affiliation(s)
- Brittany A Leigh
- University of South Florida, College of Marine Science, St. Petersburg, FL, USA; University of South Florida, Department of Pediatrics, Children's Research Institute, St. Petersburg, FL, USA
| | - Anni Djurhuus
- University of South Florida, College of Marine Science, St. Petersburg, FL, USA
| | - Mya Breitbart
- University of South Florida, College of Marine Science, St. Petersburg, FL, USA
| | - Larry J Dishaw
- University of South Florida, Department of Pediatrics, Children's Research Institute, St. Petersburg, FL, USA.
| |
Collapse
|
11
|
Leigh BA, Liberti A, Dishaw LJ. Generation of Germ-Free Ciona intestinalis for Studies of Gut-Microbe Interactions. Front Microbiol 2016; 7:2092. [PMID: 28082961 PMCID: PMC5186754 DOI: 10.3389/fmicb.2016.02092] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Accepted: 12/09/2016] [Indexed: 12/03/2022] Open
Abstract
Microbes associate with animal hosts, often providing shelter in a nutrient-rich environment. The gut, however, can be a harsh environment with members of the microbiome settling in distinct niches resulting in more stable, adherent biofilms. These diverse communities can provide orders of magnitude more gene products than the host genome; selection and maintenance of a functionally relevant and useful microbiome is now recognized to be an essential component of homeostasis. Germ-free (GF) model systems allow dissection of host-microbe interactions in a simple and direct way where each member of the symbiosis can be studied in isolation. In addition, because immune defenses in the gut are often naïve in GF animals, host immune recognition and responses during the process of colonization can be studied. Ciona intestinalis, a basal chordate, is a well-characterized developmental model system and holds promise for addressing some of these important questions. With transparent juveniles, Ciona can be exposed to distinct bacterial isolates by inoculating GF artificial seawater; concentrated bacteria can subsequently be visualized in vivo if fluorescent stains are utilized. Rearing GF Ciona is a first step in untangling the complex dialogue between bacteria and innate immunity during colonization.
Collapse
Affiliation(s)
- Brittany A Leigh
- College of Marine Science, University of South Florida (USF)St. Petersburg, FL, USA; Department of Pediatrics, College of Medicine, University of South Florida (USF)St. Petersburg, FL, USA
| | - Assunta Liberti
- Department of Pediatrics, College of Medicine, University of South Florida (USF) St. Petersburg, FL, USA
| | - Larry J Dishaw
- Department of Pediatrics, College of Medicine, University of South Florida (USF) St. Petersburg, FL, USA
| |
Collapse
|
12
|
Abstract
In the colonial tunicate Botryllus schlosseri, a co-dominant trait determines the capacity of adjacent colonies to fuse or reject. An innovative RNA sequencing approach has now identified the gene that predicts the outcomes of this naturally occurring allograft.
Collapse
Affiliation(s)
- Gary W Litman
- Morsani College of Medicine, Department of Pediatrics, University of South Florida, St. Petersburg, FL 33701, USA.
| | | |
Collapse
|
13
|
Zhang L, Li L, Guo X, Litman GW, Dishaw LJ, Zhang G. Massive expansion and functional divergence of innate immune genes in a protostome. Sci Rep 2015; 5:8693. [PMID: 25732911 PMCID: PMC4346834 DOI: 10.1038/srep08693] [Citation(s) in RCA: 176] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 02/02/2015] [Indexed: 02/06/2023] Open
Abstract
The molecules that mediate innate immunity are encoded by relatively few genes and exhibit broad specificity. Detailed annotation of the Pacific oyster (Crassostrea gigas) genome, a protostome invertebrate, reveals large-scale duplication and divergence of multigene families encoding molecules that effect innate immunity. Transcriptome analyses indicate dynamic and orchestrated specific expression of numerous innate immune genes in response to experimental challenge with pathogens, including bacteria, and a pathogenic virus. Variable expression of individual members of the multigene families encoding these genes also occurs during different types of abiotic stress (environmentally-equivalent conditions of temperature, salinity and desiccation). Multiple families of immune genes are responsive in concert to certain biotic and abiotic challenges. Individual members of expanded families of immune genes are differentially expressed under both biotic challenge and abiotic stress conditions. Members of the same families of innate immune molecules also are transcribed in developmental stage- and tissue-specific manners. An integrated, highly complex innate immune system that exhibits remarkable discriminatory properties and responses to different pathogens as well as environmental stress has arisen through the adaptive recruitment of tandem duplicated genes. The co-adaptive evolution of stress and innate immune responses appears to have an ancient origin in phylogeny.
Collapse
Affiliation(s)
- Linlin Zhang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Li Li
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Ximing Guo
- Haskin Shellfish Research Laboratory, Institute of National and Local Marine and Coastal Sciences, Rutgers University, Port Norris, NJ 08349, USA
| | - Gary W Litman
- 1] Morsani College of Medicine, Department of Pediatrics, University of South Florida, St. Petersburg, FL 33701, USA [2] All Children's Hospital Johns Hopkins Medicine, St. Petersburg, FL 33701, USA
| | - Larry J Dishaw
- Morsani College of Medicine, Department of Pediatrics, University of South Florida, St. Petersburg, FL 33701, USA
| | - Guofan Zhang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| |
Collapse
|
14
|
Dishaw LJ, Cannon JP, Litman GW, Parker W. Immune-directed support of rich microbial communities in the gut has ancient roots. Dev Comp Immunol 2014; 47:36-51. [PMID: 24984114 PMCID: PMC4146740 DOI: 10.1016/j.dci.2014.06.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 05/30/2014] [Accepted: 06/21/2014] [Indexed: 05/12/2023]
Abstract
The animal gut serves as a primary location for the complex host-microbe interplay that is essential for homeostasis and may also reflect the types of ancient selective pressures that spawned the emergence of immunity in metazoans. In this review, we present a phylogenetic survey of gut host-microbe interactions and suggest that host defense systems arose not only to protect tissue directly from pathogenic attack but also to actively support growth of specific communities of mutualists. This functional dichotomy resulted in the evolution of immune systems much more tuned for harmonious existence with microbes than previously thought, existing as dynamic but primarily cooperative entities in the present day. We further present the protochordate Ciona intestinalis as a promising model for studying gut host-bacterial dialogue. The taxonomic position, gut physiology and experimental tractability of Ciona offer unique advantages in dissecting host-microbe interplay and can complement studies in other model systems.
Collapse
Affiliation(s)
- Larry J Dishaw
- Department of Pediatrics, University of South Florida Morsani College of Medicine, USF/ACH Children's Research Institute, 140 7th Avenue South, St. Petersburg, FL 33701, USA.
| | - John P Cannon
- Department of Pediatrics, University of South Florida Morsani College of Medicine, USF/ACH Children's Research Institute, 140 7th Avenue South, St. Petersburg, FL 33701, USA
| | - Gary W Litman
- Department of Pediatrics, University of South Florida Morsani College of Medicine, USF/ACH Children's Research Institute, 140 7th Avenue South, St. Petersburg, FL 33701, USA; Department of Molecular Genetics, All Children's Hospital-Johns Hopkins Medicine, 501 6th Avenue South, St. Petersburg, FL 33701, USA
| | - William Parker
- Department of Surgery, Duke University Medical Center, Box 2605, Durham, NC 27710, USA
| |
Collapse
|
15
|
Liberti A, Melillo D, Zucchetti I, Natale L, Dishaw LJ, Litman GW, De Santis R, Pinto MR. Expression of Ciona intestinalis variable region-containing chitin-binding proteins during development of the gastrointestinal tract and their role in host-microbe interactions. PLoS One 2014; 9:e94984. [PMID: 24788831 PMCID: PMC4008424 DOI: 10.1371/journal.pone.0094984] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 03/21/2014] [Indexed: 02/04/2023] Open
Abstract
Variable region-containing chitin-binding proteins (VCBPs) are secreted, immune-type molecules that have been described in both amphioxus, a cephalochordate, and sea squirt, Ciona intestinalis, a urochordate. In adult Ciona, VCBP-A, -B and -C are expressed in hemocytes and the cells of the gastrointestinal tract. VCBP-C binds bacteria in the stomach lumen and functions as an opsonin in vitro. In the present paper the expression of VCBPs has been characterized during development using in situ hybridization, immunohistochemical staining and quantitative polymerase chain reaction (qPCR) technologies. The expression of VCBP-A and -C is detected first in discrete areas of larva endoderm and becomes progressively localized during differentiation in the stomach and intestine, marking the development of gut tracts. In “small adults” (1–2 cm juveniles) expression of VCBP-C persists and VCBP-A gradually diminishes, ultimately replaced by expression of VCBP-B. The expression of VCBP-A and -C in stage 7–8 juveniles, at which point animals have already started feeding, is influenced significantly by challenge with either Gram-positive or -negative bacteria. A potential role for VCBPs in gut-microbiota interactions and homeostasis is indicated.
Collapse
Affiliation(s)
- Assunta Liberti
- Department of Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Villa Comunale, Napoli, Italy
| | - Daniela Melillo
- Department of Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Villa Comunale, Napoli, Italy
| | - Ivana Zucchetti
- Department of Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Villa Comunale, Napoli, Italy
| | - Lenina Natale
- Department of Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Villa Comunale, Napoli, Italy
| | - Larry J. Dishaw
- Department of Pediatrics, University of South Florida College of Medicine, St Petersburg, Florida, United States of America
| | - Gary W. Litman
- Department of Pediatrics, University of South Florida College of Medicine, St Petersburg, Florida, United States of America
| | - Rosaria De Santis
- Department of Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Villa Comunale, Napoli, Italy
| | - Maria Rosaria Pinto
- Department of Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Villa Comunale, Napoli, Italy
- * E-mail:
| |
Collapse
|
16
|
Groer MW, Luciano AA, Dishaw LJ, Ashmeade TL, Miller E, Gilbert JA. Development of the preterm infant gut microbiome: a research priority. Microbiome 2014; 2:38. [PMID: 25332768 PMCID: PMC4203464 DOI: 10.1186/2049-2618-2-38] [Citation(s) in RCA: 177] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 08/30/2014] [Indexed: 05/12/2023]
Abstract
The very low birth weight (VLBW) infant is at great risk for marked dysbiosis of the gut microbiome due to multiple factors, including physiological immaturity and prenatal/postnatal influences that disrupt the development of a normal gut flora. However, little is known about the developmental succession of the microbiota in preterm infants as they grow and mature. This review provides a synthesis of our understanding of the normal development of the infant gut microbiome and contrasts this with dysbiotic development in the VLBW infant. The role of human milk in normal gut microbial development is emphasized, along with the role of the gut microbiome in immune development and gastroenteric health. Current research provides evidence that the gut microbiome interacts extensively with many physiological systems and metabolic processes in the developing infant. However, to the best of our knowledge, there are currently no studies prospectively mapping the gut microbiome of VLBW infants through early childhood. This knowledge gap must be filled to inform a healthcare system that can provide for the growth, health, and development of VLBW infants. The paper concludes with speculation about how the VLBW infants' gut microbiome might function through host-microbe interactions to contribute to the sequelae of preterm birth, including its influence on growth, development, and general health of the infant host.
Collapse
Affiliation(s)
- Maureen W Groer
- University of South Florida College of Nursing, 12910 Bruce B. Downs Blvd., Tampa, FL 33612, USA
| | - Angel A Luciano
- Department of Pediatrics, Division of Neonatology, Morsani College of Medicine, University of South Florida, Tampa General Cir, Tampa, FL 33606, USA
| | - Larry J Dishaw
- Department of Pediatrics, Morsani College of Medicine, ACH Children’s Research Institute, USF, 140 7th Avenue South, St. Petersburg, FL 33701, USA
| | - Terri L Ashmeade
- Department of Pediatrics, Division of Neonatology, Morsani College of Medicine, University of South Florida, Tampa General Cir, Tampa, FL 33606, USA
| | - Elizabeth Miller
- Department of Anthropology, University of South Florida, 4202 East Fowler Ave., Tampa, FL 33620, USA
| | - Jack A Gilbert
- Institute for Genomics and Systems Biology, Argonne National Laboratory, Lemont, IL 60439, USA
- Department of Ecology and Evolution, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, USA
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| |
Collapse
|
17
|
Affiliation(s)
- Larry J Dishaw
- Division of Molecular Genetics, Department of Pediatrics, University of South Florida Tampa, FL, USA
| | | |
Collapse
|
18
|
Dishaw LJ, Flores-Torres JA, Mueller MG, Karrer CR, Skapura DP, Melillo D, Zucchetti I, De Santis R, Pinto MR, Litman GW. A Basal chordate model for studies of gut microbial immune interactions. Front Immunol 2012; 3:96. [PMID: 22563328 PMCID: PMC3342567 DOI: 10.3389/fimmu.2012.00096] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 04/12/2012] [Indexed: 12/23/2022] Open
Abstract
Complex symbiotic interactions at the surface of host epithelia govern most encounters between host and microbe. The epithelium of the gut is a physiologically ancient structure that is comprised of a single layer of cells and is thought to possess fully developed immunological capabilities. Ciona intestinalis (sea squirt), which is a descendant of the last common ancestor of all vertebrates, is a potentially valuable model for studying barrier defenses and gut microbial immune interactions. A variety of innate immunological phenomena have been well characterized in Ciona, of which many are active in the gut tissues. Interactions with gut microbiota likely involve surface epithelium, secreted immune molecules including variable region-containing chitin-binding proteins, and hemocytes from a densely populated laminar tissue space. The microbial composition of representative gut luminal contents has been characterized by molecular screening and a potentially relevant, reproducible, dysbiosis can be induced via starvation. The dialog between host and microbe in the gut can be investigated in Ciona against the background of a competent innate immune system and in the absence of the integral elements and processes that are characteristic of vertebrate adaptive immunity.
Collapse
Affiliation(s)
- Larry J Dishaw
- Department of Pediatrics, USF/ACH Children's Research Institute, University of South Florida College of Medicine St. Petersburg, FL, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Abstract
Immune systems evolve as essential strategies to maintain homeostasis with the environment, prevent microbial assault and recycle damaged host tissues. The immune system is composed of two components, innate and adaptive immunity. The former is common to all animals while the latter consists of a vertebrate-specific system that relies on somatically derived lymphocytes and is associated with near limitless genetic diversity as well as long-term memory. Deuterostome invertebrates provide a view of immune repertoires in phyla that immediately predate the origins of vertebrates. Genomic studies in amphioxus, a cephalochordate, have revealed homologs of genes encoding most innate immune receptors found in vertebrates; however, many of the gene families have undergone dramatic expansions, greatly increasing the innate immune repertoire. In addition, domain-swapping accounts for the innovation of new predicted pathways of receptor function. In both amphioxus and Ciona, a urochordate, the VCBPs (variable region containing chitin-binding proteins), which consist of immunoglobulin V (variable) and chitin binding domains, mediate recognition through the V domains. The V domains of VCBPs in amphioxus exhibit high levels of allelic complexity that presumably relate to functional specificity. Various features of the amphioxus immune repertoire reflect novel selective pressures, which likely have resulted in innovative strategies. Functional genomic studies underscore the value of amphioxus as a model for studying innate immunity and may help reveal how unique relationships between innate immune receptors and both pathogens and symbionts factored in the evolution of adaptive immune systems.
Collapse
Affiliation(s)
- Larry J Dishaw
- Department of Pediatrics, University of South Florida, Children's Research Institute, USA
| | | | | |
Collapse
|
20
|
Dishaw LJ, Ota T, Mueller MG, Cannon JP, Haire RN, Gwatney NR, Litman RT, Litman GW. The basis for haplotype complexity in VCBPs, an immune-type receptor in amphioxus. Immunogenetics 2010; 62:623-31. [PMID: 20652563 DOI: 10.1007/s00251-010-0464-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Accepted: 07/02/2010] [Indexed: 01/04/2023]
Abstract
Innate immune gene repertoires are restricted primarily to germline variation. Adaptive immunity, by comparison, relies on somatic variation of germline-encoded genes to generate extraordinarily large numbers of non-heritable antigen recognition motifs. Invertebrates lack the key features of vertebrate adaptive immunity, but have evolved a variety of alternative mechanisms to successfully protect the integrity of "self"; in many cases, these appear to be taxon-specific innovations. In the protochordate Branchiostoma floridae (amphioxus), the variable region-containing chitin-binding proteins (VCBPs) constitute a multigene family (comprised of VCBPs 1-5), which possesses features that are consistent with innate immune-type function. A large number of VCBP alleles and haplotypes are shown to exhibit levels of polymorphism exceeding the elevated overall levels determined for the whole amphioxus genome (JGI). VCBP genes of the 2 and 5 types are distinguished further by a highly polymorphic segment (exon 2) in the N-terminal immunoglobulin domain, defined previously as a "hypervariable region" or a "hotspot." Genomic deoxyribonucleic acid (DNA) and complementary DNA (cDNA) sequences from large numbers of animals representing different populations reveal further significant differences in sequence complexity within and across VCBP2/5 haplotypes that arise through overlapping mechanisms of genetic exchange, gene copy number variation as well as mutation and give rise to distinct allelic lineages. The collective observations suggest that mechanisms were in place at the time of divergence of the cephalochordates that could selectively hyperdiversify immune-type receptors within a multigene family.
Collapse
Affiliation(s)
- Larry J Dishaw
- Department of Molecular Genetics, All Children's Hospital, St. Petersburg, FL, USA
| | | | | | | | | | | | | | | |
Collapse
|
21
|
Cannon JP, Dishaw LJ, Haire RN, Litman RT, Ostrov DA, Litman GW. Recognition of additional roles for immunoglobulin domains in immune function. Semin Immunol 2009; 22:17-24. [PMID: 20004115 DOI: 10.1016/j.smim.2009.11.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2009] [Accepted: 11/16/2009] [Indexed: 01/08/2023]
Abstract
Characterization of immune receptors found in phylogenetically disparate species at the genetic, structural and functional levels has provided unique insight into the evolutionary acquisition of immune function. The roles of variable- and intermediate-type immunoglobulin (Ig) domains in direct recognition of ligands and other functions are far wider than previously anticipated. Common mechanisms of multigene family diversification and expansion as well as unique adaptations that relate to function continue to provide unique insight into the numerous patterns, processes and complex interactions that regulate the host response to infectious challenge.
Collapse
Affiliation(s)
- John P Cannon
- University of South Florida, Department of Pediatrics, USF/ACH Children's Research Institute, 140 Seventh Avenue South, St. Petersburg, FL 33701, USA.
| | | | | | | | | | | |
Collapse
|
22
|
Dishaw LJ, Mueller MG, Gwatney N, Cannon JP, Haire RN, Litman RT, Amemiya CT, Ota T, Rowen L, Glusman G, Litman GW. Genomic complexity of the variable region-containing chitin-binding proteins in amphioxus. BMC Genet 2008; 9:78. [PMID: 19046437 PMCID: PMC2632668 DOI: 10.1186/1471-2156-9-78] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2008] [Accepted: 12/01/2008] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND The variable region-containing chitin-binding proteins (VCBPs) are found in protochordates and consist of two tandem immunoglobulin variable (V)-type domains and a chitin-binding domain. We previously have shown that these polymorphic genes, which primarily are expressed in the gut, exhibit characteristics of immune genes. In this report, we describe VCBP genomic organization and characterize adjacent and intervening genetic features which may influence both their polymorphism and complex transcriptional repertoire. RESULTS VCBP genes 1, 2, 4, and 5 are encoded in a single contiguous gene-rich chromosomal region and VCBP3 is encoded in a separate locus. The VCBPs exhibit extensive haplotype variation, including copy number variation (CNV), indel polymorphism and a markedly elevated variation in repeat type and density. In at least one haplotype, inverted repeats occur more frequently than elsewhere in the genome. Multi-animal cDNA screening, as well as transcriptional profilingusing a novel transfection system, suggests that haplotype-specific transcriptional variants may contribute to VCBP genetic diversity. CONCLUSION The availability of the Branchiostoma floridae genome (Joint Genome Institute, Brafl1), along with BAC and PAC screening and sequencing described here, reveal that the relatively limited number of VCBP genes present in the amphioxus genome exhibit exceptionally high haplotype variation. These VCBP haplotypes contribute a diverse pool of allelic variants, which includes gene copy number variation, pseudogenes, and other polymorphisms, while contributing secondary effects on gene transcription as well.
Collapse
Affiliation(s)
- Larry J Dishaw
- All Children's Hospital, Department of Molecular Genetics, 801 Sixth Street South, St. Petersburg, FL 33701, USA
- H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Avenue, Tampa, FL 33612, USA
| | - M Gail Mueller
- All Children's Hospital, Department of Molecular Genetics, 801 Sixth Street South, St. Petersburg, FL 33701, USA
| | - Natasha Gwatney
- Department of Pediatrics, University of South Florida College of Medicine, USF/ACH Children's Research Institute, 830 First Street South, St. Petersburg, FL 33701, USA
| | - John P Cannon
- H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Avenue, Tampa, FL 33612, USA
- Department of Pediatrics, University of South Florida College of Medicine, USF/ACH Children's Research Institute, 830 First Street South, St. Petersburg, FL 33701, USA
| | - Robert N Haire
- Department of Pediatrics, University of South Florida College of Medicine, USF/ACH Children's Research Institute, 830 First Street South, St. Petersburg, FL 33701, USA
| | - Ronda T Litman
- Department of Pediatrics, University of South Florida College of Medicine, USF/ACH Children's Research Institute, 830 First Street South, St. Petersburg, FL 33701, USA
| | - Chris T Amemiya
- Benaroya Research Institute, 1201 Ninth Avenue, Seattle, WA 98101, USA
| | - Tatsuya Ota
- Department of Evolutionary Studies of Biosystems, The Graduate University for Advanced Studies, Kamiyamaguchi 1560-35, Hayama 240-0193 Japan
| | - Lee Rowen
- Institute for Systems Biology, 1441 N. 34th St, Seattle, WA, 98103, USA
| | - Gustavo Glusman
- Institute for Systems Biology, 1441 N. 34th St, Seattle, WA, 98103, USA
| | - Gary W Litman
- All Children's Hospital, Department of Molecular Genetics, 801 Sixth Street South, St. Petersburg, FL 33701, USA
- H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Avenue, Tampa, FL 33612, USA
- Department of Pediatrics, University of South Florida College of Medicine, USF/ACH Children's Research Institute, 830 First Street South, St. Petersburg, FL 33701, USA
| |
Collapse
|
23
|
Holland LZ, Albalat R, Azumi K, Benito-Gutiérrez E, Blow MJ, Bronner-Fraser M, Brunet F, Butts T, Candiani S, Dishaw LJ, Ferrier DEK, Garcia-Fernàndez J, Gibson-Brown JJ, Gissi C, Godzik A, Hallböök F, Hirose D, Hosomichi K, Ikuta T, Inoko H, Kasahara M, Kasamatsu J, Kawashima T, Kimura A, Kobayashi M, Kozmik Z, Kubokawa K, Laudet V, Litman GW, McHardy AC, Meulemans D, Nonaka M, Olinski RP, Pancer Z, Pennacchio LA, Pestarino M, Rast JP, Rigoutsos I, Robinson-Rechavi M, Roch G, Saiga H, Sasakura Y, Satake M, Satou Y, Schubert M, Sherwood N, Shiina T, Takatori N, Tello J, Vopalensky P, Wada S, Xu A, Ye Y, Yoshida K, Yoshizaki F, Yu JK, Zhang Q, Zmasek CM, de Jong PJ, Osoegawa K, Putnam NH, Rokhsar DS, Satoh N, Holland PWH. The amphioxus genome illuminates vertebrate origins and cephalochordate biology. Genome Res 2008; 18:1100-11. [PMID: 18562680 DOI: 10.1101/gr.073676.107] [Citation(s) in RCA: 368] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cephalochordates, urochordates, and vertebrates evolved from a common ancestor over 520 million years ago. To improve our understanding of chordate evolution and the origin of vertebrates, we intensively searched for particular genes, gene families, and conserved noncoding elements in the sequenced genome of the cephalochordate Branchiostoma floridae, commonly called amphioxus or lancelets. Special attention was given to homeobox genes, opsin genes, genes involved in neural crest development, nuclear receptor genes, genes encoding components of the endocrine and immune systems, and conserved cis-regulatory enhancers. The amphioxus genome contains a basic set of chordate genes involved in development and cell signaling, including a fifteenth Hox gene. This set includes many genes that were co-opted in vertebrates for new roles in neural crest development and adaptive immunity. However, where amphioxus has a single gene, vertebrates often have two, three, or four paralogs derived from two whole-genome duplication events. In addition, several transcriptional enhancers are conserved between amphioxus and vertebrates--a very wide phylogenetic distance. In contrast, urochordate genomes have lost many genes, including a diversity of homeobox families and genes involved in steroid hormone function. The amphioxus genome also exhibits derived features, including duplications of opsins and genes proposed to function in innate immunity and endocrine systems. Our results indicate that the amphioxus genome is elemental to an understanding of the biology and evolution of nonchordate deuterostomes, invertebrate chordates, and vertebrates.
Collapse
Affiliation(s)
- Linda Z Holland
- Marine Biology Research Division, Scripps Institution of Oceanography, La Jolla, California 92093-0202, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Litman GW, Cannon JP, Dishaw LJ, Haire RN, Eason DD, Yoder JA, Prada JH, Ostrov DA. Immunoglobulin variable regions in molecules exhibiting characteristics of innate and adaptive immune receptors. Immunol Res 2008; 38:294-304. [PMID: 17917037 DOI: 10.1007/s12026-007-0014-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/1999] [Revised: 11/30/1999] [Accepted: 11/30/1999] [Indexed: 11/25/2022]
Abstract
The antigen combining sites of immunoglobulin (Ig) and T cell antigen receptors (TCRs), which are present in all jawed vertebrates, consist of a paired variable (V) domain heterodimer that exhibits varying degrees of germline- and extraordinarily high levels of somatically-derived variation. The near limitless variation in receptor specificity on the surface of individual lymphocytes is the basis for clonal selection in the adaptive immune response. A basic question arises as to whether or not there are other forms of immune-type receptors in vertebrates as well as in invertebrates that derive immune specificity through sequence differences in V domains. Our laboratory has discovered two such families of molecules, the novel immune-type receptors and the variable region-containing chitin-binding proteins. Both families of molecules encode V domains that share some characteristics of adaptive immune receptors but likely mediate innate functions.
Collapse
Affiliation(s)
- Gary W Litman
- Department of Pediatrics, University of South Florida College of Medicine, USF/ACH Children's Research Institute, 830 First Street South, St. Petersburg, FL 33701, USA.
| | | | | | | | | | | | | | | |
Collapse
|
25
|
Litman GW, Dishaw LJ, Cannon JP, Haire RN, Rast JP. Alternative mechanisms of immune receptor diversity. Curr Opin Immunol 2007; 19:526-34. [PMID: 17703932 PMCID: PMC2065753 DOI: 10.1016/j.coi.2007.07.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2007] [Revised: 07/02/2007] [Accepted: 07/02/2007] [Indexed: 01/30/2023]
Abstract
Our views of both innate and adaptive immunity have been significantly modified by recent studies of immune receptors and immunity in protostomes, invertebrate deuterostomes, and jawless vertebrates. Extraordinary variation in the means whereby organisms recognize pathogens has been revealed by a series of recent findings, including: novel forms of familiar immune receptors, high genetic polymorphism for new receptor types, germline rearrangement for non-Ig domain receptors, somatic variation of germline-encoded receptors, and unusually complex alternative splicing of genes with both immune and non-immune roles. Collectively, these observations underscore heretofore unrecognized pathways in the evolution of immune recognition and suggest universal processes by which immune systems co-opt and integrate existing cellular mechanisms to effect diverse recognition functions.
Collapse
Affiliation(s)
- Gary W Litman
- Department of Molecular Genetics, All Children's Hospital, 801 Sixth Street South, St. Petersburg, FL 33701, United States.
| | | | | | | | | |
Collapse
|
26
|
Dorsey MJ, Petrovic A, Morrow MR, Sleasman JW, Dishaw LJ. Foxp3 Expression Following Bone Marrow Transplantation for IPEX Syndrome After Reduced-Intensity Conditioning. Clin Immunol 2007. [DOI: 10.1016/j.clim.2007.03.299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
27
|
Dishaw LJ, Herrera ML, Bigger CH. Characterization and phylogenetic analysis of a cnidarian LMP X-like cDNA. Immunogenetics 2006; 58:454-64. [PMID: 16552514 DOI: 10.1007/s00251-006-0105-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2005] [Accepted: 02/15/2006] [Indexed: 12/01/2022]
Abstract
Proteasomes are multisubunit protease complexes which are partly responsible for metabolism of intracellular, ubiquitinylated proteins. Vertebrates have adapted a second and specialized structure responsible for the generation of peptides presented to the adaptive immune system and is thus, commonly referred to as the immunoproteasome. This complex is assembled from paralogous copies of subunits belonging to the constitutive, housekeeping proteasome. The immunoproteasome is more efficient in the generation of peptides for display on major histocompatibility complex (MHC) molecules. Important components of this complex are the paralogous members, LMP X and 7; where the latter replaces the former in the assembly of the immunoproteasome of vertebrates. In this report, we describe an LMP X-like cDNA from an endosymbiont-free gorgonian coral, Swiftia exserta. Cnidarians predate the phylogenetic divergence of protostomes and deuterostomes (P-D split), and are becoming an essential model for our comprehension of immune system evolution. Phylogenetic analyses of available sequences indicates that invertebrate LMP X-like sequences are outgroups to vertebrate LMP X and LMP 7, and is in agreement with previous observations that the duplication event giving rise to the two rapidly diverging lineages of proteasomal subunits occurred before jawed fished divergence.
Collapse
Affiliation(s)
- Larry J Dishaw
- Department of Biological Sciences, Florida International University, Miami, FL, 33199, USA
| | | | | |
Collapse
|
28
|
Abstract
Numerous studies of the mammalian immune system have begun to uncover profound interrelationships, as well as fundamental differences, between the adaptive and innate systems of immune recognition. Coincident with these investigations, the increasing experimental accessibility of non-mammalian jawed vertebrates, jawless vertebrates, protochordates and invertebrates has provided intriguing new information regarding the likely patterns of emergence of immune-related molecules during metazoan phylogeny, as well as the evolution of alternative mechanisms for receptor diversification. Such findings blur traditional distinctions between adaptive and innate immunity and emphasize that, throughout evolution, the immune system has used a remarkably extensive variety of solutions to meet fundamentally similar requirements for host protection.
Collapse
MESH Headings
- Animals
- Evolution, Molecular
- Gene Rearrangement, B-Lymphocyte/genetics
- Gene Rearrangement, B-Lymphocyte/immunology
- Gene Rearrangement, T-Lymphocyte/genetics
- Gene Rearrangement, T-Lymphocyte/immunology
- Genes, Immunoglobulin/genetics
- Genes, Immunoglobulin/immunology
- Genes, RAG-1/immunology
- Immunity, Innate/genetics
- Immunity, Innate/immunology
- Invertebrates/genetics
- Invertebrates/immunology
- Phylogeny
- Receptors, Immunologic/genetics
- Receptors, Immunologic/immunology
- Vertebrates/genetics
- Vertebrates/immunology
Collapse
Affiliation(s)
- Gary W Litman
- Department of Pediatrics, University of South Florida College of Medicine, All Children's Hospital Children's Research Institute, 830 First Street South, Saint Petersburg, Florida 33701, USA.
| | | | | |
Collapse
|
29
|
Dishaw LJ, Smith SL, Bigger CH. Characterization of a C3-like cDNA in a coral: phylogenetic implications. Immunogenetics 2005; 57:535-48. [PMID: 16041540 DOI: 10.1007/s00251-005-0005-1] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2004] [Accepted: 05/19/2005] [Indexed: 11/26/2022]
Abstract
C3, C4, and C5 are thiolester-containing proteins (TEPs) of vertebrate complement. The identification of the molecular origin of the TEP family, and more specifically the ancestor protein of complement components C3, C4, and C5, remains a fundamental question. The prevailing paradigm suggests that duplication and divergence of these proteins occurred after the deuterostome split in phylogeny. It is believed that the ancestor of thiolester-containing complement proteins was alpha-2-macroglobulin (A2M)-like, a noncomplement-related protein. Here we describe a C3-like cDNA from a gorgonian coral, Swiftia exserta. This study provides evidence for the origins of a complement-related C3-like gene in the Precambrian period, predating both protostomes and deuterostomes. Furthermore, one may speculate that complement-like opsonic reactions were evolving at the earliest stages of metazoan evolution. This calls for a reassessment of the present concepts concerning the origins and evolution of TEPs.
Collapse
Affiliation(s)
- Larry J Dishaw
- Department of Biological Sciences, Florida International University, University Park Campus, 11200 SW 8th Street, Miami, FL 33199, USA
| | | | | |
Collapse
|
30
|
Kozmik Z, Daube M, Frei E, Norman B, Kos L, Dishaw LJ, Noll M, Piatigorsky J. Role of Pax genes in eye evolution: a cnidarian PaxB gene uniting Pax2 and Pax6 functions. Dev Cell 2003; 5:773-85. [PMID: 14602077 DOI: 10.1016/s1534-5807(03)00325-3] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
PaxB from Tripedalia cystophora, a cubomedusan jellyfish possessing complex eyes (ocelli), was characterized. PaxB, the only Pax gene found in this cnidarian, is expressed in the larva, retina, lens, and statocyst. PaxB contains a Pax2/5/8-type paired domain and octapeptide, but a Pax6 prd-type homeodomain. Pax2/5/8-like properties of PaxB include a DNA binding specificity of the paired domain, activation and inhibitory domains, and the ability to rescue spa(pol), a Drosophila Pax2 eye mutant. Like Pax6, PaxB activates jellyfish crystallin and Drosophila rhodopsin rh6 promoters and induces small ectopic eyes in Drosophila. Pax6 has been considered a "master" control gene for eye development. Our data suggest that the ancestor of jellyfish PaxB, a PaxB-like protein, was the primordial Pax protein in eye evolution and that Pax6-like genes evolved in triploblasts after separation from Cnidaria, raising the possibility that cnidarian and sophisticated triploblastic eyes arose independently.
Collapse
Affiliation(s)
- Zbynek Kozmik
- Laboratory of Molecular and Developmental Biology, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | | | | | | | | | | | | |
Collapse
|
31
|
Piatigorsky J, Norman B, Dishaw LJ, Kos L, Horwitz J, Steinbach PJ, Kozmik Z. J3-crystallin of the jellyfish lens: similarity to saposins. Proc Natl Acad Sci U S A 2001; 98:12362-7. [PMID: 11675486 PMCID: PMC60059 DOI: 10.1073/pnas.231310698] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2001] [Indexed: 11/18/2022] Open
Abstract
J3-crystallin, one of the three major eye-lens proteins of the cubomedusan jellyfish (Tripedalia cystophora), shows similarity to vertebrate saposins, which are multifunctional proteins that bridge lysosomal hydrolases to lipids and activate enzyme activity. Sequence alignment of deduced J3-crystallin indicates two saposin-like motifs arranged in tandem, each containing six cysteines characteristic of this protein family. The J3-crystallin cDNA encodes a putative precursor analogous to vertebrate prosaposins. The J3-crystallin gene has seven exons, with exons 2-4 encoding the protein. Exon 3 encodes a circularly permutated saposin motif, called a swaposin, found in plant aspartic proteases. J3-crystallin RNA was found in the cubomedusan lens, statocyst, in bands radiating from the pigmented region of the ocellus, in the tentacle tip by in situ hybridization, and in the embryo and larva by reverse transcription-PCR. Our data suggest a crystallin role for the multifunctional saposin protein family in the jellyfish lens. This finding extends the gene sharing evolutionary strategy for lens crystallins to the cnidarians and indicates that the putative primordial saposin/swaposin J3-crystallin reflects both the chaperone and enzyme connections of the vertebrate crystallins.
Collapse
Affiliation(s)
- J Piatigorsky
- Laboratory of Molecular and Developmental Biology, National Eye Institute, and Center for Molecular Modeling, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892, USA.
| | | | | | | | | | | | | |
Collapse
|