1
|
Smith LC. The marine sponge, Hymeniacidon sinapium, displays allorecognition of siblings during post-larval settling and metamorphosis to juveniles. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2024; 157:105179. [PMID: 38614378 DOI: 10.1016/j.dci.2024.105179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/15/2024]
Abstract
Marine sponges, including the crumb of bread sponge, Hymeniacidon sinapium, display allorejection responses to contact with conspecifics in both experimental and natural settings. These responses have been used to infer immunocompetence in a variety of marine invertebrates. However, larvae and juveniles from several marine sponge species fuse and form chimeras. Some of these chimeras persist, whereas others eventually break down, revealing a period of allogeneic non-responsiveness that varies depending on the species. Alternatively, for H. sinapium, most pairs of sibling post-larvae and juveniles that settle in contact initiate immediate allorecognition and show the same morphological response progression as the adults. This indicates that allorecognition and response occurs during early metamorphosis. Results from H. sinapium and other sponge species, in addition to annotations of sponge genomes, suggest that allorecognition and immunocompetence in sponges are mediated by distinct systems and may become functional at different times during or after metamorphosis for different species. Consequently, allorecognition may not be a good proxy for the onset of immunocompetence.
Collapse
Affiliation(s)
- L Courtney Smith
- The Department of Microbiology and Immunology, University of California at Los Angeles, 609 Charles E Young Drive E, Los Angeles, CA, 90024, USA; The Department of Biological Sciences, George Washington University, Suite 6000, 800 22nd St NW, Washington, DC, 20052, USA.
| |
Collapse
|
2
|
Marulanda-Gomez AM, Ribes M, Franzenburg S, Hentschel U, Pita L. Transcriptomic responses of Mediterranean sponges upon encounter with symbiont microbial consortia. BMC Genomics 2024; 25:674. [PMID: 38972970 PMCID: PMC11229196 DOI: 10.1186/s12864-024-10548-z] [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: 03/06/2024] [Accepted: 06/21/2024] [Indexed: 07/09/2024] Open
Abstract
BACKGROUND Sponges (phylum Porifera) constantly interact with microbes. They graze on microbes from the water column by filter-feeding and they harbor symbiotic partners within their bodies. In experimental setups, sponges take up symbionts at lower rates compared with seawater microbes. This suggests that sponges have the capacity to differentiate between microbes and preferentially graze in non-symbiotic microbes, although the underlying mechanisms of discrimination are still poorly understood. Genomic studies showed that, compared to other animal groups, sponges present an extended repertoire of immune receptors, in particular NLRs, SRCRs, and GPCRs, and a handful of experiments showed that sponges regulate the expression of these receptors upon encounter with microbial elicitors. We hypothesize that sponges may rely on differential expression of their diverse repertoire of poriferan immune receptors to sense different microbial consortia while filter-feeding. To test this, we characterized the transcriptomic response of two sponge species, Aplysina aerophoba and Dysidea avara, upon incubation with microbial consortia extracted from A. aerophoba in comparison with incubation with seawater microbes. The sponges were sampled after 1 h, 3 h, and 5 h for RNA-Seq differential gene expression analysis. RESULTS D. avara incubated with A. aerophoba-symbionts regulated the expression of genes related to immunity, ubiquitination, and signaling. Within the set of differentially-expressed immune genes we identified different families of Nucleotide Oligomerization Domain (NOD)-Like Receptors (NLRs). These results represent the first experimental evidence that different types of NLRs are involved in microbial discrimination in a sponge. In contrast, the transcriptomic response of A. aerophoba to its own symbionts involved comparatively fewer genes and lacked genes encoding for immune receptors. CONCLUSION Our work suggests that: (i) the transcriptomic response of sponges upon microbial exposure may imply "fine-tuning" of baseline gene expression as a result of their interaction with microbes, (ii) the differential response of sponges to microbial encounters varied between the species, probably due to species-specific characteristics or related to host's traits, and (iii) immune receptors belonging to different families of NLR-like genes played a role in the differential response to microbes, whether symbionts or food bacteria. The regulation of these receptors in sponges provides further evidence of the potential role of NLRs in invertebrate host-microbe interactions. The study of sponge responses to microbes exemplifies how investigating different animal groups broadens our knowledge of the evolution of immune specificity and symbiosis.
Collapse
Affiliation(s)
| | - Marta Ribes
- Institut de Ciències del Mar, ICM - CSIC, Barcelona, Spain
| | - Sören Franzenburg
- Research Group Genetics and Bioinformatics/Systems Immunology, Institute of Clinical Molecular Biology, Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Ute Hentschel
- RD3 Marine Ecology, RU Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Lucia Pita
- Institut de Ciències del Mar, ICM - CSIC, Barcelona, Spain.
| |
Collapse
|
3
|
Schäfer Y, Palitzsch K, Leptin M, Whiteley AR, Wiehe T, Suurväli J. Copy number variation and population-specific immune genes in the model vertebrate zebrafish. eLife 2024; 13:e98058. [PMID: 38832644 PMCID: PMC11192531 DOI: 10.7554/elife.98058] [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: 03/28/2024] [Accepted: 06/03/2024] [Indexed: 06/05/2024] Open
Abstract
Copy number variation in large gene families is well characterized for plant resistance genes, but similar studies are rare in animals. The zebrafish (Danio rerio) has hundreds of NLR immune genes, making this species ideal for studying this phenomenon. By sequencing 93 zebrafish from multiple wild and laboratory populations, we identified a total of 1513 NLRs, many more than the previously known 400. Approximately half of those are present in all wild populations, but only 4% were found in 80% or more of the individual fish. Wild fish have up to two times as many NLRs per individual and up to four times as many NLRs per population than laboratory strains. In contrast to the massive variability of gene copies, nucleotide diversity in zebrafish NLR genes is very low: around half of the copies are monomorphic and the remaining ones have very few polymorphisms, likely a signature of purifying selection.
Collapse
Affiliation(s)
| | | | - Maria Leptin
- Institute for Genetics, University of CologneCologneGermany
| | - Andrew R Whiteley
- WA Franke College of Forestry and Conservation, University of MontanaMissoulaUnited States
| | - Thomas Wiehe
- Institute for Genetics, University of CologneCologneGermany
| | - Jaanus Suurväli
- Institute for Genetics, University of CologneCologneGermany
- Department of Biological Sciences, University of ManitobaWinnipegCanada
| |
Collapse
|
4
|
Gama AR, Miller T, Venkatesan S, Lange JJ, Wu J, Song X, Bradford D, Unruh JR, Halfmann R. Protein supersaturation powers innate immune signaling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.03.20.533581. [PMID: 36993308 PMCID: PMC10055258 DOI: 10.1101/2023.03.20.533581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Innate immunity protects us in youth but turns against us as we age. The reason for this tradeoff is unclear. Seeking a thermodynamic basis, we focused on death fold domains (DFDs), whose ordered polymerization has been stoichiometrically linked to innate immune signal amplification. We hypothesized that soluble ensembles of DFDs function as phase change batteries that store energy via supersaturation and subsequently release it through nucleated polymerization. Using imaging and FRET-based cytometry to characterize the phase behaviors of all 109 human DFDs, we found that the hubs of innate immune signaling networks encode large nucleation barriers that are intrinsically insulated from cross-pathway activation. We showed via optogenetics that supersaturation drives signal amplification and that the inflammasome is constitutively supersaturated in vivo. Our findings reveal that the soluble "inactive" states of adaptor DFDs function as essential, yet impermanent, kinetic barriers to inflammatory cell death, suggesting a thermodynamic driving force for aging.
Collapse
Affiliation(s)
| | - Tayla Miller
- Stowers Institute for Medical Research, Kansas City, MO
| | | | | | - Jianzheng Wu
- Stowers Institute for Medical Research, Kansas City, MO
| | - Xiaoqing Song
- Stowers Institute for Medical Research, Kansas City, MO
| | - Dan Bradford
- Stowers Institute for Medical Research, Kansas City, MO
| | - Jay R Unruh
- Stowers Institute for Medical Research, Kansas City, MO
| | - Randal Halfmann
- Stowers Institute for Medical Research, Kansas City, MO
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, USA
| |
Collapse
|
5
|
Pan JM, Liang Y, Zhu KC, Guo HY, Liu BS, Zhang N, Zhang DC. Identification of the NOD-like receptor family of golden pompano and expression in response to bacterial and parasitic exposure reveal its key role in innate immunity. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2024; 152:105123. [PMID: 38135022 DOI: 10.1016/j.dci.2023.105123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/01/2023] [Accepted: 12/15/2023] [Indexed: 12/24/2023]
Abstract
This study presents a genome-wide identification of NOD-like receptors (NLRs) in the golden pompano, key to its innate immunity. We identified 30 ToNLRs, analyzing their chromosomal positions, characteristics, evolutionary relationships, evidence of positive selection, and synteny with the yellowtail kingfish. Our findings categorize these NLRs into three main subgroups: NLRA, NLRC, and the distinct ToNLRX1. Post-exposure to Streptococcus agalactiae, most ToNLRs increased expression in the spleen, whereas NLRC3like13, NLRC3like16, and NLRC3like19 so in the kidneys. Upon Cryptocaryon irritans exposure, we categorized our groups based on the site of infection into the control group (BFS), the trophont-attached skin (TAS), and the nearby region skin (NRS). ToAPAF1 and ToNOD1 expressions rose in the NRS, in contrast to decreased expressions of ToNLRC5, ToNWD1 and ToCIITA. Other ToNLRs showed variable expressions in the TAS. Overall, this research lays the groundwork for further exploration of innate immunity in the golden pompano.
Collapse
Affiliation(s)
- Jin-Min Pan
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300, Guangzhou, Guangdong Province, PR China
| | - Yu Liang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300, Guangzhou, Guangdong Province, PR China
| | - Ke-Cheng Zhu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300, Guangzhou, Guangdong Province, PR China; Sanya Tropical Fisheries Research Institute, Sanya, 572018, PR China; Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, Guangdong Province, PR China
| | - Hua-Yang Guo
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300, Guangzhou, Guangdong Province, PR China; Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, Guangdong Province, PR China
| | - Bao-Suo Liu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300, Guangzhou, Guangdong Province, PR China; Sanya Tropical Fisheries Research Institute, Sanya, 572018, PR China; Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, Guangdong Province, PR China
| | - Nan Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300, Guangzhou, Guangdong Province, PR China; Sanya Tropical Fisheries Research Institute, Sanya, 572018, PR China; Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, Guangdong Province, PR China
| | - Dian-Chang Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300, Guangzhou, Guangdong Province, PR China; Sanya Tropical Fisheries Research Institute, Sanya, 572018, PR China; Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, Guangdong Province, PR China.
| |
Collapse
|
6
|
Silva RCMC, Gomes FM. Evolution of the Major Components of Innate Immunity in Animals. J Mol Evol 2024; 92:3-20. [PMID: 38281163 DOI: 10.1007/s00239-024-10155-2] [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: 10/28/2023] [Accepted: 01/11/2024] [Indexed: 01/30/2024]
Abstract
Innate immunity is present in all animals. In this review, we explore the main conserved mechanisms of recognition and innate immune responses among animals. In this sense, we discuss the receptors, critical for binding to pathogen-associated molecular patterns (PAMPs) or danger-associated molecular patterns (DAMPs); the downstream signaling proteins; and transcription factors that govern immune responses. We also highlight conserved inflammatory mediators that are induced after the recognition of DAMPs and PAMPs. At last, we discuss the mechanisms that are involved in the regulation and/or generation of reactive oxygen species (ROS), influencing immune responses, like heme-oxygenases (HOs).
Collapse
Affiliation(s)
- Rafael Cardoso Maciel Costa Silva
- Laboratory of Immunoreceptors and Signaling, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Fábio Mendonça Gomes
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| |
Collapse
|
7
|
Peng Z, Zhang W, Fu H, Li Y, Zhang C, Li J, Chan J, Zhang L. Genome-Wide Comparative Analysis of SRCR Gene Superfamily in Invertebrates Reveals Massive and Independent Gene Expansions in the Sponge and Sea Urchin. Int J Mol Sci 2024; 25:1515. [PMID: 38338794 PMCID: PMC10855680 DOI: 10.3390/ijms25031515] [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: 11/17/2023] [Revised: 01/12/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
Without general adaptative immunity, invertebrates evolved a vast number of heterogeneous non-self recognition strategies. One of those well-known adaptations is the expansion of the immune receptor gene superfamily coding for scavenger receptor cysteine-rich domain containing proteins (SRCR) in a few invertebrates. Here, we investigated the evolutionary history of the SRCR gene superfamily (SRCR-SF) across 29 metazoan species with an emphasis on invertebrates. We analyzed their domain architectures, genome locations and phylogenetic distribution. Our analysis shows extensive genome-wide duplications of the SRCR-SFs in Amphimedon queenslandica and Strongylocentrotus purpuratus. Further molecular evolution study reveals various patterns of conserved cysteines in the sponge and sea urchin SRCR-SFs, indicating independent and convergent evolution of SRCR-SF expansion during invertebrate evolution. In the case of the sponge SRCR-SFs, a novel motif with seven conserved cysteines was identified. Exon-intron structure analysis suggests the rapid evolution of SRCR-SFs during gene duplications in both the sponge and the sea urchin. Our findings across nine representative metazoans also underscore a heightened expression of SRCR-SFs in immune-related tissues, notably the digestive glands. This observation indicates the potential role of SRCR-SFs in reinforcing distinct immune functions in these invertebrates. Collectively, our results reveal that gene duplication, motif structure variation, and exon-intron divergence might lead to the convergent evolution of SRCR-SF expansions in the genomes of the sponge and sea urchin. Our study also suggests that the utilization of SRCR-SF receptor duplication may be a general and basal strategy to increase immune diversity and tissue specificity for the invertebrates.
Collapse
Affiliation(s)
- Zhangjie Peng
- College of Life Sciences, School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China; (Z.P.); (H.F.); (Y.L.); (C.Z.)
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- College of Marine Science, University of Chinese Academy of Sciences, Beijing 100049, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Wei Zhang
- College of Life Sciences, School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China; (Z.P.); (H.F.); (Y.L.); (C.Z.)
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Hailun Fu
- College of Life Sciences, School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China; (Z.P.); (H.F.); (Y.L.); (C.Z.)
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yuzhu Li
- College of Life Sciences, School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China; (Z.P.); (H.F.); (Y.L.); (C.Z.)
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Chunyu Zhang
- College of Life Sciences, School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China; (Z.P.); (H.F.); (Y.L.); (C.Z.)
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Jie Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- College of Marine Science, University of Chinese Academy of Sciences, Beijing 100049, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Qingdao 266071, China
| | - Jiulin Chan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Qingdao 266071, China
| | - Linlin Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- College of Marine Science, University of Chinese Academy of Sciences, Beijing 100049, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Qingdao 266071, China
| |
Collapse
|
8
|
Castel B, El Mahboubi K, Jacquet C, Delaux PM. Immunobiodiversity: Conserved and specific immunity across land plants and beyond. MOLECULAR PLANT 2024; 17:92-111. [PMID: 38102829 DOI: 10.1016/j.molp.2023.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/20/2023] [Accepted: 12/12/2023] [Indexed: 12/17/2023]
Abstract
Angiosperms represent most plants that humans cultivate, grow, and eat. However, angiosperms are only one of five major land plant lineages. As a whole lineage, plants also include algal groups. All these clades represent a tremendous genetic diversity that can be investigated to reveal the evolutionary history of any given mechanism. In this review, we describe the current model of the plant immune system, discuss its evolution based on the recent literature, and propose future directions for the field. In angiosperms, plant-microbe interactions have been intensively studied, revealing essential cell surface and intracellular immune receptors, as well as metabolic and hormonal defense pathways. Exploring diversity at the genomic and functional levels demonstrates the conservation of these pathways across land plants, some of which are beyond plants. On basis of the conserved mechanisms, lineage-specific variations have occurred, leading to diversified reservoirs of immune mechanisms. In rare cases, this diversity has been harnessed and successfully transferred to other species by integration of wild immune receptors or engineering of novel forms of receptors for improved resistance to pathogens. We propose that exploring further the diversity of immune mechanisms in the whole plant lineage will reveal completely novel sources of resistance to be deployed in crops.
Collapse
Affiliation(s)
- Baptiste Castel
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, Toulouse INP, Castanet-Tolosan, France
| | - Karima El Mahboubi
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, Toulouse INP, Castanet-Tolosan, France
| | - Christophe Jacquet
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, Toulouse INP, Castanet-Tolosan, France
| | - Pierre-Marc Delaux
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, Toulouse INP, Castanet-Tolosan, France.
| |
Collapse
|
9
|
Aizpurua O, Blijleven K, Trivedi U, Gilbert MTP, Alberdi A. Unravelling animal-microbiota evolution on a chip. Trends Microbiol 2023; 31:995-1002. [PMID: 37217368 DOI: 10.1016/j.tim.2023.04.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/25/2023] [Accepted: 04/28/2023] [Indexed: 05/24/2023]
Abstract
Whether and how microorganisms have shaped the evolution of their animal hosts is a major question in biology. Although many animal evolutionary processes appear to correlate with changes in their associated microbial communities, the mechanistic processes leading to these patterns and their causal relationships are still far from being resolved. Gut-on-a-chip models provide an innovative approach that expands beyond the potential of conventional microbiome profiling to study how different animals sense and react to microbes by comparing responses of animal intestinal tissue models to different microbial stimuli. This complementary knowledge can contribute to our understanding of how host genetic features facilitate or prevent different microbiomes from being assembled, and in doing so elucidate the role of host-microbiota interactions in animal evolution.
Collapse
Affiliation(s)
- Ostaizka Aizpurua
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Kees Blijleven
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Urvish Trivedi
- Department of Biology, Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark; University Museum, NTNU, Trondheim, Norway
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
10
|
Chia K, Carella P. Taking the lead: NLR immune receptor N-terminal domains execute plant immune responses. THE NEW PHYTOLOGIST 2023; 240:496-501. [PMID: 37525357 PMCID: PMC10952240 DOI: 10.1111/nph.19170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 07/05/2023] [Indexed: 08/02/2023]
Abstract
Nucleotide-binding domain and leucine-rich repeat (NLR) proteins are important intracellular immune receptors that activate robust plant immune responses upon detecting pathogens. Canonical NLRs consist of a conserved tripartite architecture that includes a central regulatory nucleotide-binding domain, C-terminal leucine-rich repeats, and variable N-terminal domains that directly participate in immune execution. In flowering plants, the vast majority of NLR N-terminal domains belong to the coiled-coil, Resistance to Powdery Mildew 8, or Toll/interleukin-1 receptor subfamilies, with recent structural and biochemical studies providing detailed mechanistic insights into their functions. In this insight review, we focus on the immune-related biochemistries of known plant NLR N-terminal domains and discuss the evolutionary diversity of atypical NLR domains in nonflowering plants. We further contrast these observations against the known diversity of NLR-related receptors from microbes to metazoans across the tree of life.
Collapse
Affiliation(s)
- Khong‐Sam Chia
- Cell and Developmental BiologyJohn Innes CentreColney LaneNorwichNR4 7UHUK
| | - Philip Carella
- Cell and Developmental BiologyJohn Innes CentreColney LaneNorwichNR4 7UHUK
| |
Collapse
|
11
|
Rousset F, Yirmiya E, Nesher S, Brandis A, Mehlman T, Itkin M, Malitsky S, Millman A, Melamed S, Sorek R. A conserved family of immune effectors cleaves cellular ATP upon viral infection. Cell 2023; 186:3619-3631.e13. [PMID: 37595565 DOI: 10.1016/j.cell.2023.07.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 05/18/2023] [Accepted: 07/12/2023] [Indexed: 08/20/2023]
Abstract
During viral infection, cells can deploy immune strategies that deprive viruses of molecules essential for their replication. Here, we report a family of immune effectors in bacteria that, upon phage infection, degrade cellular adenosine triphosphate (ATP) and deoxyadenosine triphosphate (dATP) by cleaving the N-glycosidic bond between the adenine and sugar moieties. These ATP nucleosidase effectors are widely distributed within multiple bacterial defense systems, including cyclic oligonucleotide-based antiviral signaling systems (CBASS), prokaryotic argonautes, and nucleotide-binding leucine-rich repeat (NLR)-like proteins, and we show that ATP and dATP degradation during infection halts phage propagation. By analyzing homologs of the immune ATP nucleosidase domain, we discover and characterize Detocs, a family of bacterial defense systems with a two-component phosphotransfer-signaling architecture. The immune ATP nucleosidase domain is also encoded within diverse eukaryotic proteins with immune-like architectures, and we show biochemically that eukaryotic homologs preserve the ATP nucleosidase activity. Our findings suggest that ATP and dATP degradation is a cell-autonomous innate immune strategy conserved across the tree of life.
Collapse
Affiliation(s)
- Francois Rousset
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Erez Yirmiya
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Shahar Nesher
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Alexander Brandis
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tevie Mehlman
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Maxim Itkin
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sergey Malitsky
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Adi Millman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sarah Melamed
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Rotem Sorek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.
| |
Collapse
|
12
|
Riesgo A, Santodomingo N, Koutsouveli V, Kumala L, Leger MM, Leys SP, Funch P. Molecular machineries of ciliogenesis, cell survival, and vasculogenesis are differentially expressed during regeneration in explants of the demosponge Halichondria panicea. BMC Genomics 2022; 23:858. [PMID: 36581804 PMCID: PMC9798719 DOI: 10.1186/s12864-022-09035-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 11/21/2022] [Indexed: 12/30/2022] Open
Abstract
Sponges are interesting animal models for regeneration studies, since even from dissociated cells, they are able to regenerate completely. In particular, explants are model systems that can be applied to many sponge species, since small fragments of sponges can regenerate all elements of the adult, including the oscula and the ability to pump water. The morphological aspects of regeneration in sponges are relatively well known, but the molecular machinery is only now starting to be elucidated for some sponge species. Here, we have used an explant system of the demosponge Halichondria panicea to understand the molecular machinery deployed during regeneration of the aquiferous system. We sequenced the transcriptomes of four replicates of the 5-day explant without an osculum (NOE), four replicates of the 17-18-day explant with a single osculum and pumping activity (PE) and also four replicates of field-collected individuals with regular pumping activity (PA), and performed differential gene expression analysis. We also described the morphology of NOE and PE samples using light and electron microscopy. Our results showed a highly disorganised mesohyl and disarranged aquiferous system in NOE that is coupled with upregulated pathways of ciliogenesis, organisation of the ECM, and cell proliferation and survival. Once the osculum is formed, genes involved in "response to stimulus in other organisms" were upregulated. Interestingly, the main molecular machinery of vasculogenesis described in vertebrates was activated during the regeneration of the aquiferous system. Notably, vasculogenesis markers were upregulated when the tissue was disorganised and about to start forming canals (NOE) and angiogenic stimulators and ECM remodelling machineries were differentially expressed once the aquiferous system was in place (PE and PA). Our results are fundamental to better understanding the molecular mechanisms involved in the formation of the aquiferous system in sponges, and its similarities with the early onset of blood-vessel formation in animal evolution.
Collapse
Affiliation(s)
- Ana Riesgo
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (CSIC), Calle José Gutiérrez Abascal 2, 28006, Madrid, Spain.
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW5 7BD, UK.
| | - Nadia Santodomingo
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW5 7BD, UK
- Department of Earth Sciences, Oxford University, South Parks Road, Oxford, OX1 3AN, UK
| | - Vasiliki Koutsouveli
- Marine Symbioses Research Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, D-24105, Kiel, Germany
| | - Lars Kumala
- Nordcee, Department of Biology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
- Marine Biological Research Center, University of Southern Denmark, Hindsholmvej 11, 5300, Kerteminde, Denmark
| | - Michelle M Leger
- Institute of Evolutionary Biology (CSIC-UPF), Paseo Marítimo de la Barceloneta 37-49, 08003, Barcelona, Spain
| | - Sally P Leys
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, Alberta, T6G 2R3, Canada
| | - Peter Funch
- Department of Biology, Aarhus University, Ny Munkegade, 114-116, Aarhus C, Denmark
| |
Collapse
|
13
|
Chuphal B, Rai U, Roy B. Teleost NOD-like receptors and their downstream signaling pathways: A brief review. FISH AND SHELLFISH IMMUNOLOGY REPORTS 2022; 3:100056. [DOI: 10.1016/j.fsirep.2022.100056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/01/2022] [Accepted: 05/02/2022] [Indexed: 02/08/2023] Open
|
14
|
Wu X, Chen J, Wang X, Shang Y, Wei Q, Zhang H. Evolutionary Impacts of Pattern Recognition Receptor Genes on Carnivora Complex Habitat Stress Adaptation. Animals (Basel) 2022; 12:ani12233331. [PMID: 36496853 PMCID: PMC9739989 DOI: 10.3390/ani12233331] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/22/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022] Open
Abstract
Many mammals develop specific immune responses owing to the changes in their ecological niche and diet that are essential for animal survival. However, pattern recognition receptors (PRRs) serve as the first line of defense in innate immunity and generate immune responses in the host. However, the evolutionary impacts on PRR genes in Carnivora are not well studied. Herein, we explored the evolution of 946 PRR gene sequences in 43 Carnivora species to elucidate the molecular mechanisms of carnivore adaptation to complex habitats. We found that the PRRs were relatively conserved, and different gene families showed different evolutionary patterns. PRRs were highly purified based on their overall roles in Carnivora species but interspersed with positive-selection patterns during evolution. Different niche types may have jointly driven the evolution of PRR genes. In particular, the selection pressure of toll-like receptor (TLR) 10 was relaxed in seven species with pseudogenes, which may have emerged during recent evolutionary events. We speculated that a "functional compensation" mechanism may exist for genes with overlapping functions in the TLR gene family. Additionally, TLR2, TLR4, NLRC5, and DECTIN1 were subject to positive selection in semi-aquatic species, and the adaptive evolution of these genes may have been related to the adaptation to semi-aquatic environments. In summary, our findings offer valuable insights into the molecular and functional evolution of PRR genes, which are important for immune adaptations in Carnivora.
Collapse
Affiliation(s)
- Xiaoyang Wu
- College of Life Sciences, Qufu Normal University, Qufu 273165, China
| | - Jun Chen
- College of Marine Life Sciences, Ocean University of China, Qingdao 266005, China
| | - Xibao Wang
- College of Life Sciences, Qufu Normal University, Qufu 273165, China
| | - Yongquan Shang
- College of Life Sciences, Qufu Normal University, Qufu 273165, China
| | - Qinguo Wei
- College of Life Sciences, Qufu Normal University, Qufu 273165, China
| | - Honghai Zhang
- College of Life Sciences, Qufu Normal University, Qufu 273165, China
- Correspondence:
| |
Collapse
|
15
|
Barela Hudgell MA, Smith LC. The complex set of internal repeats in SpTransformer protein sequences result in multiple but limited alternative alignments. Front Immunol 2022; 13:1000177. [PMID: 36330505 PMCID: PMC9623053 DOI: 10.3389/fimmu.2022.1000177] [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: 07/21/2022] [Accepted: 09/23/2022] [Indexed: 11/13/2022] Open
Abstract
The SpTransformer (SpTrf) gene family encodes a set of proteins that function in the sea urchin immune system. The gene sequences have a series of internal repeats in a mosaic pattern that is characteristic of this family. This mosaic pattern necessitates the insertion of large gaps, which has made alignments of the deduced protein sequences computationally difficult such that only manual alignments have been reported previously. Because manual alignments are time consuming for evaluating newly available SpTrf sequences, computational approaches were evaluated for the sequences reported previously. Furthermore, because two different manual alignments of the SpTrf sequences are feasible because of the multiple internal repeats, it is not known whether additional alternative alignments can be identified using different approaches. The bioinformatic program, PRANK, was used because it was designed to align sequences with large gaps and indels. The results from PRANK show that the alignments of the internal repeats are similar to those done manually, suggesting multiple feasible alignments for some regions. GUIDANCE based analysis of the alignments identified regions that were excellent and other regions that failed to align. This suggests that computational approaches have limits for aligning the SpTrf sequences that include multiple repeats and that require inserted gaps. Furthermore, it is unlikely that alternative alignments for the full-length SpTrf sequences will be identified.
Collapse
|
16
|
Innate Immunity Mechanisms in Marine Multicellular Organisms. Mar Drugs 2022; 20:md20090549. [PMID: 36135738 PMCID: PMC9505182 DOI: 10.3390/md20090549] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/19/2022] [Accepted: 08/22/2022] [Indexed: 11/27/2022] Open
Abstract
The innate immune system provides an adequate response to stress factors and pathogens through pattern recognition receptors (PRRs), located on the surface of cell membranes and in the cytoplasm. Generally, the structures of PRRs are formed by several domains that are evolutionarily conserved, with a fairly high degree of homology in representatives of different species. The orthologs of TLRs, NLRs, RLRs and CLRs are widely represented, not only in marine chordates, but also in invertebrates. Study of the interactions of the most ancient marine multicellular organisms with microorganisms gives us an idea of the evolution of molecular mechanisms of protection against pathogens and reveals new functions of already known proteins in ensuring the body’s homeostasis. The review discusses innate immunity mechanisms of protection of marine invertebrate organisms against infections, using the examples of ancient multicellular hydroids, tunicates, echinoderms, and marine worms in the context of searching for analogies with vertebrate innate immunity. Due to the fact that mucous membranes first arose in marine invertebrates that have existed for several hundred million years, study of their innate immune system is both of fundamental importance in terms of understanding molecular mechanisms of host defense, and of practical application, including the search of new antimicrobial agents for subsequent use in medicine, veterinary and biotechnology.
Collapse
|
17
|
Zhu X, Mu K, Wan Y, Zhang L. Evolutionary history of the NLR gene families across lophotrochozoans. Gene 2022; 843:146807. [PMID: 35964873 DOI: 10.1016/j.gene.2022.146807] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 08/01/2022] [Accepted: 08/06/2022] [Indexed: 11/29/2022]
Abstract
NOD-like receptor (NLR) genes are critical innate immune receptors in animals and plants. Lophotrochozoans represent one of the most species-rich superphyla that includes molluscs, segmented worms, flatworms, bryozoans, and other invertebrates, which is crucial to our understanding of immune system evolution in bilaterians. However, NLRs have not been systematically described in lophotrochozoans. We annotated 185 NLRs in 29 lophotrochozoan genomes, and analyzed their domain organization, phylogenetic distribution, molecular evolution, and gene expression. We found that all the 24 molluscan genomes studied encoded no more than three NLRs. None of these molluscan NLRs represented an inducible expression pattern under the infection of eight pathogens; some molluscan NLRs showed developmental stage-specific expression patterns. Instead, 29 molluscan incomplete NLR (incNLR) genes, encoding for proteins absent in the NACHT domain were upregulated under pathogen infection. We also documented the species-specific expansion of NLRs in the clades Polychaeta and Pteriidae. Our study revealed that gene duplication, domain shuffling, gene loss, and novel expression pattern played important roles in the molecular evolution of NLRs.
Collapse
Affiliation(s)
- Xiaofei Zhu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China; CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Kang Mu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China
| | - Yi Wan
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Linlin Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
18
|
Li X, Li S, Sun M, Yu Y, Zhang X, Xiang J, Li F. A newly identified NLR-like gene participates in bacteria and virus infection possibly through regulating hemocytes apoptosis in shrimp. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2022; 132:104395. [PMID: 35288120 DOI: 10.1016/j.dci.2022.104395] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 06/14/2023]
Abstract
The nucleotide-binding oligomerization domain (NOD)-like receptors (NLRs) play important roles in innate immunity. Previously, we identified an NLR-like gene, LvNLRPL1, and found that it participated in Vibrio infection and regulated hemocytes apoptosis in the Pacific whiteleg shrimp Litopenaeus vannamei. However, it is still unclear whether other NLR-like genes exist in shrimp and how they function during virus infection. In the present study, a novel NLR-like gene (LvNLRPL2) was identified and functionally characterized in L. vannamei. LvNLRPL2 was highly expressed in hemocytes and responsive to both Vibrio parahaemolyticus and white spot syndrome virus (WSSV) infection. Knockdown of LvNLRPL2 could markedly increase the proliferation of Vibrio and the mortality of shrimp infected with V. parahaemolyticus, whereas inhibit in vivo WSSV propagation in shrimp, indicating its distinct roles during Vibrio and WSSV infection. After LvNLRPL2 knockdown, the apoptotic rate of hemocytes increased, and the expression levels of LvCaspase 2, 3 and 5 were significantly up-regulated. In addition, LvNLRPL2 could form a hetero-dimer with LvNLRPL1 through their NACHT domains. These results suggest that LvNLRPL2 might resist bacterial infection while promote WSSV propagation by forming hetero-dimer with LvNLRPL1 and then inhibiting apoptosis of hemocytes. These data will be helpful for understanding the functions of NLR-like genes and their regulation mechanisms in crustaceans.
Collapse
Affiliation(s)
- Xuechun Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shihao Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China.
| | - Mingzhe Sun
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yang Yu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Xiaojun Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Jianhai Xiang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Fuhua Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan 430072, China.
| |
Collapse
|
19
|
Abstract
Introduction Neutrophilic granulocytes are short‐lived cells continuously circulating in the vascular system of vertebrates. They play a basic and decisive role in the innate immune defence of the hosts against all types of pathogenic microorganisms. Methods Based on a literature study, the functions of neutrophils and cells with similar functions are described. The study places special emphasis on organisms in the aquatic environment and the pathogens occurring in that particular environment. Results The evolutionary origin of this specific cell type is not clear, but its most basic traits (recognition of foreign elements, extracellular trap release, phagocytosis and elimination of ingested material) are found in phagocytes in members of evolutionary ancient invertebrate groups spanning from amoebae, sponges, sea‐anemones, mollusks (snails and mussels), arthropods (crustaceans and insects) to echinoderms (sea stars and sea urchins). Their functions as innate immune sentinels and effector cells in these groups are well described. Neutrophilic granulocytes with elongated and lobed nuclei (possibly allowing cell movements through narrow extracellular spaces and leaving space for phagosomes) occur in vertebrates including fish, amphibians, reptiles, birds and mammals although the morphology of the nucleus, stainability of cytoplasmic granula, and the antimicrobial armament vary among groups. Following the pathogen invasion of a fish host, the neutrophils migrates from the vascular system into the infection focus. They apply their PRRs (including TLRs) to recognize the invader as non‐self, produce netosis by casting extracellular chromatin containing traps in the microenvironment. These nets assist the immobilization of invading microbes and prevents their further spread. The cells attach to and engulf the microbes by phagocytosis, whereafter they eliminate the pathogen in phagolysosomes equipped with a range of killing mechanisms and attract, by release of chemokines, additional immune cells (monocytes, macrophages and lymphocytes) to the site of invasion. Their role in innate immunity of fish hosts towards aquatic pathogens has been elucidated by in vivo and in vitro studies. Neutrophils interact with virus (e.g. IPNV and VHSV), bacteria (e.g. Aeromonas, Vibrio, Edwardsiella, Mycobacterium and Renibacterium) and parasites, including monogeneans (Gyrodactylus), cestodes (Diphyllobothrium), trematodes (Diplostomum) and ciliates (Ichthyophthirius and Philasterides). Despite the decisive function of neutrophils in innate immunity and early protection, the excessive production of ROS, RNS and NETs may lead to pathological disturbances in the host, which are exacerbated if the pathogens evolve immune evasion mechanisms. Conclusion Neutrophils in aquatic organisms play a central role in innate immunity but may serve as a toll and a support in acquired protection. The strong impact of the cellular reactions not only on pathogen but also on host tissues emphasizes that an optimal immune reaction is balanced, involves targeted and specific effector mechanisms, which leaves a minimum of collateral damage in host organs.
Collapse
Affiliation(s)
- Kurt Buchmann
- Laboratory of Aquatic Pathobiology, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| |
Collapse
|
20
|
Zhang L, He J, Tan P, Gong Z, Qian S, Miao Y, Zhang HY, Tu G, Chen Q, Zhong Q, Han G, He J, Wang M. The genome of an apodid holothuroid (Chiridota heheva) provides insights into its adaptation to a deep-sea reducing environment. Commun Biol 2022; 5:224. [PMID: 35273345 PMCID: PMC8913654 DOI: 10.1038/s42003-022-03176-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 02/16/2022] [Indexed: 11/09/2022] Open
Abstract
Cold seeps and hydrothermal vents are deep-sea reducing environments that are characterized by lacking oxygen and photosynthesis-derived nutrients. Most animals acquire nutrition in cold seeps or hydrothermal vents by maintaining epi- or endosymbiotic relationship with chemoautotrophic microorganisms. Although several seep- and vent-dwelling animals hosting symbiotic microbes have been well-studied, the genomic basis of adaptation to deep-sea reducing environment in nonsymbiotic animals is still lacking. Here, we report a high-quality genome of Chiridota heheva Pawson & Vance, 2004, which thrives by extracting organic components from sediment detritus and suspended material, as a reference for nonsymbiotic animal's adaptation to deep-sea reducing environments. The expansion of the aerolysin-like protein family in C. heheva compared with other echinoderms might be involved in the disintegration of microbes during digestion. Moreover, several hypoxia-related genes (Pyruvate Kinase M2, PKM2; Phospholysine Phosphohistidine Inorganic Pyrophosphate Phosphatase, LHPP; Poly(A)-specific Ribonuclease Subunit PAN2, PAN2; and Ribosomal RNA Processing 9, RRP9) were subject to positive selection in the genome of C. heheva, which contributes to their adaptation to hypoxic environments.
Collapse
Affiliation(s)
- Long Zhang
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China
| | - Jian He
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China
| | - Peipei Tan
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China
| | - Zhen Gong
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Shiyu Qian
- School of Medicine, Jinan University, Guangzhou, 510632, China
| | - Yuanyuan Miao
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China
| | - Han-Yu Zhang
- Hainan Key Laboratory of Marine Georesource and Prospecting, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China
| | - Guangxian Tu
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China
| | - Qi Chen
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China
| | - Qiqi Zhong
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China
| | - Guanzhu Han
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Jianguo He
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China. .,Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China. .,Maoming Branch, Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Maoming, 525435, China.
| | - Muhua Wang
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China. .,Maoming Branch, Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Maoming, 525435, China.
| |
Collapse
|
21
|
Li X, Li S, Yu Y, Zhang X, Xiang J, Li F. The immune function of a NLR like gene, LvNLRPL1, in the Pacific whiteleg shrimp Litopenaeus vannamei. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2022; 128:104311. [PMID: 34752843 DOI: 10.1016/j.dci.2021.104311] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/03/2021] [Accepted: 11/04/2021] [Indexed: 06/13/2023]
Abstract
NOD-like receptors (NLRs) are a kind of pattern recognition receptors, which are vital for detection of pathogen-associated molecular patterns (PAMPs) or damage-associated molecular patterns (DAMPs) and then trigger downstream immune responses in vertebrates. Although many NLR like genes have been identified in invertebrates in recent years, knowledge about their immune functions is still very limited. In the present study, a NLR like gene, designated as LvNLRPL1, was identified in Litopenaeus vannamei. It was widely expressed in multiple tissues and responsive to the infection of Vibrio parahaemolyticus. Knockdown of LvNLRPL1 could accelerate the proliferation of Vibrio in hepatopancreas and increase the mortality rate of shrimp after Vibrio infection. Meanwhile, knockdown of LvNLRPL1 also up-regulated the expression of Caspase 2, 3 and 5 in hemocytes, which caused apoptosis of more hemocytes. These results indicated that LvNLRPL1 played important immune functions in shrimp during Vibrio infection through regulating the apoptosis of hemocytes in shrimp. To our knowledge, this is the first time to reveal the immune function of a NLR like gene in crustaceans.
Collapse
Affiliation(s)
- Xuechun Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shihao Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China.
| | - Yang Yu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Xiaojun Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Jianhai Xiang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Fuhua Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan 430072, China.
| |
Collapse
|
22
|
Hui F, Guo S, Liu J, Li M, Geng M, Xia Y, Liu X, Li Q, Li J, Zhu T. Genome-wide identification and characterization of NLR genes in lamprey (Lethenteron reissneri) and their responses to lipopolysaccharide/poly(I:C) challenge. Mol Immunol 2022; 143:122-134. [DOI: 10.1016/j.molimm.2022.01.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 12/18/2022]
|
23
|
Posadas N, Baquiran JIP, Nada MAL, Kelly M, Conaco C. Microbiome diversity and host immune functions influence survivorship of sponge holobionts under future ocean conditions. THE ISME JOURNAL 2022; 16:58-67. [PMID: 34218251 PMCID: PMC8692459 DOI: 10.1038/s41396-021-01050-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 06/20/2021] [Accepted: 06/23/2021] [Indexed: 02/06/2023]
Abstract
The sponge-associated microbial community contributes to the overall health and adaptive capacity of the sponge holobiont. This community is regulated by the environment and the immune system of the host. However, little is known about the effect of environmental stress on the regulation of host immune functions and how this may, in turn, affect sponge-microbe interactions. In this study, we compared the bacterial diversity and immune repertoire of the demosponge, Neopetrosia compacta, and the calcareous sponge, Leucetta chagosensis, under varying levels of acidification and warming stress based on climate scenarios predicted for 2100. Neopetrosia compacta harbors a diverse microbial community and possesses a rich repertoire of scavenger receptors while L. chagosensis has a less diverse microbiome and an expanded range of pattern recognition receptors and immune response-related genes. Upon exposure to RCP 8.5 conditions, the microbiome composition and host transcriptome of N. compacta remained stable, which correlated with high survival (75%). In contrast, tissue necrosis and low survival (25%) of L. chagosensis was accompanied by microbial community shifts and downregulation of host immune-related pathways. Meta-analysis of microbiome diversity and immunological repertoire across poriferan classes further highlights the importance of host-microbe interactions in predicting the fate of sponges under future ocean conditions.
Collapse
Affiliation(s)
- Niño Posadas
- grid.11134.360000 0004 0636 6193Marine Science Institute, University of the Philippines Diliman, Quezon City, Philippines
| | - Jake Ivan P. Baquiran
- grid.11134.360000 0004 0636 6193Marine Science Institute, University of the Philippines Diliman, Quezon City, Philippines
| | - Michael Angelou L. Nada
- grid.11134.360000 0004 0636 6193Marine Science Institute, University of the Philippines Diliman, Quezon City, Philippines
| | - Michelle Kelly
- grid.419676.b0000 0000 9252 5808National Institute of Water and Atmospheric Research, Ltd., Auckland, New Zealand
| | - Cecilia Conaco
- grid.11134.360000 0004 0636 6193Marine Science Institute, University of the Philippines Diliman, Quezon City, Philippines
| |
Collapse
|
24
|
Recurrent expansions of B30.2-associated immune receptor families in fish. Immunogenetics 2021; 74:129-147. [PMID: 34850255 DOI: 10.1007/s00251-021-01235-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 11/16/2021] [Indexed: 12/12/2022]
Abstract
B30.2 domains, also known as PRY/SPRY, are key components of specific subsets of two large families of proteins involved in innate immunity: the tripartite motif proteins (TRIMs) and the Nod-like receptors (NLRs). TRIM proteins are important, often inducible factors of antiviral innate immunity, targeting multiple steps of viral cycles through a variety of mechanisms. NLRs prime and regulate systemic innate defenses, especially against bacteria, and control inflammation. Large TRIM and NLR subsets characterized by the presence of a B30.2 domain have been reported from a few fish species including zebrafish and seem to be strongly prone to gene duplication/expansion. Here, we performed a large-scale survey of these receptors across about 150 fish genomes, focusing on ray-finned fishes. We assessed the number and genomic distribution of domains and domain combinations associated with TRIMs, NLRs, and other genes containing B30.2 domains and looked for gene expansion patterns across fish groups. We then used a model to test the impact of taxonomy, genome size, and environmental variables on the copy numbers of these genes. Our findings reveal novel domain structures, clade-specific gains and losses. They also assist with the timing of the gene expansions, reveal patterns associated with the MHC, and lay the groundwork for further studies delving deeper into the forces that drive the copy number variation of immune genes on a species level.
Collapse
|
25
|
Barela Hudgell MA, Smith LC. Sequence Diversity, Locus Structure, and Evolutionary History of the SpTransformer Genes in the Sea Urchin Genome. Front Immunol 2021; 12:744783. [PMID: 34867968 PMCID: PMC8634487 DOI: 10.3389/fimmu.2021.744783] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 10/12/2021] [Indexed: 11/13/2022] Open
Abstract
The generation of large immune gene families is often driven by evolutionary pressure exerted on host genomes by their pathogens, which has been described as the immunological arms race. The SpTransformer (SpTrf) gene family from the California purple sea urchin, Strongylocentrotus purpuratus, is upregulated upon immune challenge and encodes the SpTrf proteins that interact with pathogens during an immune response. Native SpTrf proteins bind both bacteria and yeast, and augment phagocytosis of a marine Vibrio, while a recombinant SpTrf protein (rSpTrf-E1) binds a subset of pathogens and a range of pathogen associated molecular patterns. In the sequenced sea urchin genome, there are four SpTrf gene clusters for a total of 17 genes. Here, we report an in-depth analysis of these genes to understand the sequence complexities of this family, its genomic structure, and to derive a putative evolutionary history for the formation of the gene clusters. We report a detailed characterization of gene structure including the intron type and UTRs with conserved transcriptional start sites, the start codon and multiple stop codons, and locations of polyadenylation signals. Phylogenetic and percent mismatch analyses of the genes and the intergenic regions allowed us to predict the last common ancestral SpTrf gene and a theoretical evolutionary history of the gene family. The appearance of the gene clusters from the theoretical ancestral gene may have been driven by multiple duplication and deletion events of regions containing SpTrf genes. Duplications and ectopic insertion events, indels, and point mutations in the exons likely resulted in the extant genes and family structure. This theoretical evolutionary history is consistent with the involvement of these genes in the arms race in responses to pathogens and suggests that the diversification of these genes and their encoded proteins have been selected for based on the survival benefits of pathogen binding and host protection.
Collapse
Affiliation(s)
| | - L. Courtney Smith
- Department of Biological Sciences, George Washington University, Washington, DC, United States
| |
Collapse
|
26
|
Tassia MG, David KT, Townsend JP, Halanych KM. TIAMMAt: Leveraging biodiversity to revise protein domain models, evidence from innate immunity. Mol Biol Evol 2021; 38:5806-5818. [PMID: 34459919 PMCID: PMC8662601 DOI: 10.1093/molbev/msab258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Sequence annotation is fundamental for studying the evolution of protein families, particularly when working with nonmodel species. Given the rapid, ever-increasing number of species receiving high-quality genome sequencing, accurate domain modeling that is representative of species diversity is crucial for understanding protein family sequence evolution and their inferred function(s). Here, we describe a bioinformatic tool called Taxon-Informed Adjustment of Markov Model Attributes (TIAMMAt) which revises domain profile hidden Markov models (HMMs) by incorporating homologous domain sequences from underrepresented and nonmodel species. Using innate immunity pathways as a case study, we show that revising profile HMM parameters to directly account for variation in homologs among underrepresented species provides valuable insight into the evolution of protein families. Following adjustment by TIAMMAt, domain profile HMMs exhibit changes in their per-site amino acid state emission probabilities and insertion/deletion probabilities while maintaining the overall structure of the consensus sequence. Our results show that domain revision can heavily impact evolutionary interpretations for some families (i.e., NLR’s NACHT domain), whereas impact on other domains (e.g., rel homology domain and interferon regulatory factor domains) is minimal due to high levels of sequence conservation across the sampled phylogenetic depth (i.e., Metazoa). Importantly, TIAMMAt revises target domain models to reflect homologous sequence variation using the taxonomic distribution under consideration by the user. TIAMMAt’s flexibility to revise any subset of the Pfam database using a user-defined taxonomic pool will make it a valuable tool for future protein evolution studies, particularly when incorporating (or focusing) on nonmodel species.
Collapse
Affiliation(s)
- Michael G Tassia
- Department of Biological Sciences, Auburn University, Auburn, Alabama
| | - Kyle T David
- Department of Biological Sciences, Auburn University, Auburn, Alabama
| | - James P Townsend
- Whitman Center, Marine Biological Laboratory, Woods Hole, Massachusetts.,Department of Biology, Providence College, Providence, Rhode Island
| | | |
Collapse
|
27
|
Tan M, Redmond AK, Dooley H, Nozu R, Sato K, Kuraku S, Koren S, Phillippy AM, Dove ADM, Read T. The whale shark genome reveals patterns of vertebrate gene family evolution. eLife 2021; 10:e65394. [PMID: 34409936 PMCID: PMC8455134 DOI: 10.7554/elife.65394] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 08/18/2021] [Indexed: 02/06/2023] Open
Abstract
Chondrichthyes (cartilaginous fishes) are fundamental for understanding vertebrate evolution, yet their genomes are understudied. We report long-read sequencing of the whale shark genome to generate the best gapless chondrichthyan genome assembly yet with higher contig contiguity than all other cartilaginous fish genomes, and studied vertebrate genomic evolution of ancestral gene families, immunity, and gigantism. We found a major increase in gene families at the origin of gnathostomes (jawed vertebrates) independent of their genome duplication. We studied vertebrate pathogen recognition receptors (PRRs), which are key in initiating innate immune defense, and found diverse patterns of gene family evolution, demonstrating that adaptive immunity in gnathostomes did not fully displace germline-encoded PRR innovation. We also discovered a new toll-like receptor (TLR29) and three NOD1 copies in the whale shark. We found chondrichthyan and giant vertebrate genomes had decreased substitution rates compared to other vertebrates, but gene family expansion rates varied among vertebrate giants, suggesting substitution and expansion rates of gene families are decoupled in vertebrate genomes. Finally, we found gene families that shifted in expansion rate in vertebrate giants were enriched for human cancer-related genes, consistent with gigantism requiring adaptations to suppress cancer.
Collapse
Affiliation(s)
- Milton Tan
- Illinois Natural History Survey at University of Illinois Urbana-ChampaignChampaignUnited States
| | | | - Helen Dooley
- University of Maryland School of Medicine, Institute of Marine & Environmental TechnologyBaltimoreUnited States
| | - Ryo Nozu
- Okinawa Churashima Research Center, Okinawa Churashima FoundationOkinawaJapan
| | - Keiichi Sato
- Okinawa Churashima Research Center, Okinawa Churashima FoundationOkinawaJapan
- Okinawa Churaumi Aquarium, MotobuOkinawaJapan
| | - Shigehiro Kuraku
- RIKEN Center for Biosystems Dynamics Research (BDR), RIKENKobeJapan
| | - Sergey Koren
- National Human Genome Research Institute, National Institutes of HealthBethesdaUnited States
| | - Adam M Phillippy
- National Human Genome Research Institute, National Institutes of HealthBethesdaUnited States
| | | | - Timothy Read
- Department of Infectious Diseases, Emory University School of MedicineAtlantaUnited States
| |
Collapse
|
28
|
Mandujano-Tinoco EA, Sultan E, Ottolenghi A, Gershoni-Yahalom O, Rosental B. Evolution of Cellular Immunity Effector Cells; Perspective on Cytotoxic and Phagocytic Cellular Lineages. Cells 2021; 10:1853. [PMID: 34440622 PMCID: PMC8394812 DOI: 10.3390/cells10081853] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 12/14/2022] Open
Abstract
The immune system has evolved to protect organisms from infections caused by bacteria, viruses, and parasitic pathogens. In addition, it provides regenerative capacities, tissue maintenance, and self/non-self recognition of foreign tissues. Phagocytosis and cytotoxicity are two prominent cellular immune activities positioned at the base of immune effector function in mammals. Although these immune mechanisms have diversified into a wide heterogeneous repertoire of effector cells, it appears that they share some common cellular and molecular features in all animals, but also some interesting convergent mechanisms. In this review, we will explore the current knowledge about the evolution of phagocytic and cytotoxic immune lineages against pathogens, in the clearance of damaged cells, for regeneration, for histocompatibility recognition, and in killing virally infected cells. To this end, we give different immune examples of multicellular organism models, ranging from the roots of bilateral organisms to chordate invertebrates, comparing to vertebrates' lineages. In this review, we compare cellular lineage homologies at the cellular and molecular levels. We aim to highlight and discuss the diverse function plasticity within the evolved immune effector cells, and even suggest the costs and benefits that it may imply for organisms with the meaning of greater defense against pathogens but less ability to regenerate damaged tissues and organs.
Collapse
Affiliation(s)
- Edna Ayerim Mandujano-Tinoco
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, and Regenerative Medicine and Stem Cell Research Center, Ben Gurion University of the Negev, Beer Sheva 8410501, Israel; (E.S.); (A.O.); (O.G.-Y.)
- Laboratory of Connective Tissue, Centro Nacional de Investigación y Atención de Quemados, Instituto Nacional de Rehabilitación “Luis Guillermo Ibarra Ibarra”, Calzada Mexico-Xochimilco No. 289, Col. Arenal de Guadalupe, Tlalpan, Mexico City 14389, Mexico
| | - Eliya Sultan
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, and Regenerative Medicine and Stem Cell Research Center, Ben Gurion University of the Negev, Beer Sheva 8410501, Israel; (E.S.); (A.O.); (O.G.-Y.)
| | - Aner Ottolenghi
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, and Regenerative Medicine and Stem Cell Research Center, Ben Gurion University of the Negev, Beer Sheva 8410501, Israel; (E.S.); (A.O.); (O.G.-Y.)
| | - Orly Gershoni-Yahalom
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, and Regenerative Medicine and Stem Cell Research Center, Ben Gurion University of the Negev, Beer Sheva 8410501, Israel; (E.S.); (A.O.); (O.G.-Y.)
| | - Benyamin Rosental
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, and Regenerative Medicine and Stem Cell Research Center, Ben Gurion University of the Negev, Beer Sheva 8410501, Israel; (E.S.); (A.O.); (O.G.-Y.)
| |
Collapse
|
29
|
Emery MA, Dimos BA, Mydlarz LD. Cnidarian Pattern Recognition Receptor Repertoires Reflect Both Phylogeny and Life History Traits. Front Immunol 2021; 12:689463. [PMID: 34248980 PMCID: PMC8260672 DOI: 10.3389/fimmu.2021.689463] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/07/2021] [Indexed: 12/12/2022] Open
Abstract
Pattern recognition receptors (PRRs) are evolutionarily ancient and crucial components of innate immunity, recognizing danger-associated molecular patterns (DAMPs) and activating host defenses. Basal non-bilaterian animals such as cnidarians must rely solely on innate immunity to defend themselves from pathogens. By investigating cnidarian PRR repertoires we can gain insight into the evolution of innate immunity in these basal animals. Here we utilize the increasing amount of available genomic resources within Cnidaria to survey the PRR repertoires and downstream immune pathway completeness within 15 cnidarian species spanning two major cnidarian clades, Anthozoa and Medusozoa. Overall, we find that anthozoans possess prototypical PRRs, while medusozoans appear to lack these immune proteins. Additionally, anthozoans consistently had higher numbers of PRRs across all four classes relative to medusozoans, a trend largely driven by expansions in NOD-like receptors and C-type lectins. Symbiotic, sessile, and colonial cnidarians also have expanded PRR repertoires relative to their non-symbiotic, mobile, and solitary counterparts. Interestingly, cnidarians seem to lack key components of mammalian innate immune pathways, though similar to PRR numbers, anthozoans possess more complete immune pathways than medusozoans. Together, our data indicate that anthozoans have greater immune specificity than medusozoans, which we hypothesize to be due to life history traits common within Anthozoa. Overall, this investigation reveals important insights into the evolution of innate immune proteins within these basal animals.
Collapse
Affiliation(s)
- Madison A Emery
- Department of Biology, University of Texas at Arlington, Arlington, TX, United States
| | - Bradford A Dimos
- Department of Biology, University of Texas at Arlington, Arlington, TX, United States
| | - Laura D Mydlarz
- Department of Biology, University of Texas at Arlington, Arlington, TX, United States
| |
Collapse
|
30
|
Duxbury Z, Wu CH, Ding P. A Comparative Overview of the Intracellular Guardians of Plants and Animals: NLRs in Innate Immunity and Beyond. ANNUAL REVIEW OF PLANT BIOLOGY 2021; 72:155-184. [PMID: 33689400 DOI: 10.1146/annurev-arplant-080620-104948] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Nucleotide-binding domain leucine-rich repeat receptors (NLRs) play important roles in the innate immune systems of both plants and animals. Recent breakthroughs in NLR biochemistry and biophysics have revolutionized our understanding of how NLR proteins function in plant immunity. In this review, we summarize the latest findings in plant NLR biology and draw direct comparisons to NLRs of animals. We discuss different mechanisms by which NLRs recognize their ligands in plants and animals. The discovery of plant NLR resistosomes that assemble in a comparable way to animal inflammasomes reinforces the striking similarities between the formation of plant and animal NLR complexes. Furthermore, we discuss the mechanisms by which plant NLRs mediate immune responses and draw comparisons to similar mechanisms identified in animals. Finally, we summarize the current knowledge of the complex genetic architecture formed by NLRs in plants and animals and the roles of NLRs beyond pathogen detection.
Collapse
Affiliation(s)
- Zane Duxbury
- Jealott's Hill International Research Centre, Syngenta, Bracknell RG42 6EY, United Kingdom;
| | - Chih-Hang Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan;
| | - Pingtao Ding
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
- Current affiliation: Institute of Biology Leiden, Leiden University, Leiden 2333 BE, The Netherlands;
| |
Collapse
|
31
|
Schmittmann L, Franzenburg S, Pita L. Individuality in the Immune Repertoire and Induced Response of the Sponge Halichondria panicea. Front Immunol 2021; 12:689051. [PMID: 34220847 PMCID: PMC8242945 DOI: 10.3389/fimmu.2021.689051] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/28/2021] [Indexed: 12/16/2022] Open
Abstract
The animal immune system mediates host-microbe interactions from the host perspective. Pattern recognition receptors (PRRs) and the downstream signaling cascades they induce are a central part of animal innate immunity. These molecular immune mechanisms are still not fully understood, particularly in terms of baseline immunity vs induced specific responses regulated upon microbial signals. Early-divergent phyla like sponges (Porifera) can help to identify the evolutionarily conserved mechanisms of immune signaling. We characterized both the expressed immune gene repertoire and the induced response to lipopolysaccharides (LPS) in Halichondria panicea, a promising model for sponge symbioses. We exposed sponges under controlled experimental conditions to bacterial LPS and performed RNA-seq on samples taken 1h and 6h after exposure. H. panicea possesses a diverse array of putative PRRs. While part of those PRRs was constitutively expressed in all analyzed sponges, the majority was expressed individual-specific and regardless of LPS treatment or timepoint. The induced immune response by LPS involved differential regulation of genes related to signaling and recognition, more specifically GTPases and post-translational regulation mechanisms like ubiquitination and phosphorylation. We have discovered individuality in both the immune receptor repertoire and the response to LPS, which may translate into holobiont fitness and susceptibility to stress. The three different layers of immune gene control observed in this study, - namely constitutive expression, individual-specific expression, and induced genes -, draw a complex picture of the innate immune gene regulation in H. panicea. Most likely this reflects synergistic interactions among the different components of immunity in their role to control and respond to a stable microbiome, seawater bacteria, and potential pathogens.
Collapse
Affiliation(s)
- Lara Schmittmann
- Research Unit Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Sören Franzenburg
- Research Group Genetics&Bioinformatics/Systems Immunology, Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - Lucía Pita
- Research Unit Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| |
Collapse
|
32
|
Chang MX, Xiong F, Wu XM, Hu YW. The expanding and function of NLRC3 or NLRC3-like in teleost fish: Recent advances and novel insights. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 114:103859. [PMID: 32896535 DOI: 10.1016/j.dci.2020.103859] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/31/2020] [Accepted: 08/31/2020] [Indexed: 06/11/2023]
Abstract
The nucleotide-binding domain and leucine-rich repeat-containing family (NLR) proteins are innate immune sensors which recognize highly conserved pathogen-associated molecular patterns (PAMPs). Mammals have small numbers of NLR proteins, whereas in some species such as in invertebrates and jawless vertebrates, NLRs have expanded into very large families. Nearly 400 NLR proteins are identified in the zebrafish genome. Members of the NLR family can be divided into two functional sub-groups based on their ability to either positively or negatively regulate host immune response or inflammatory signaling cascades. Mammalian NLRC3 has been identified as an inhibitory NLR, and serves as a negative regulator in the NF-κB-mediated inflammatory response, STING-mediated DNA sensing and PI3K-mTOR pathways. Different from mammalian NLRC3, the analysis from genomes or transcriptomes revealed that the expansions of NLRC3 existed in different species of fish. Furthermore, piscine NLRC3-like genes were confirmed to have a negative or positive regulatory function in response to different kinds of pathogen infections and in the production of proinflammatory cytokines. In this review, we summarize recent advances in our understanding of the expanding and function of NLRC3 or NLRC3-like genes in teleost fish, and give our view of important directions for future studies. The knowledge of piscine NLRC3 or expansive NLRC3-like genes-mediated biological functions in homeostasis and diseases will shed new light on the prevention and control of inflammatory and/or infectious diseases.
Collapse
Affiliation(s)
- Ming Xian Chang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Aquaculture Disease Control, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, 430072, China; Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China.
| | - Fan Xiong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Aquaculture Disease Control, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, 430072, China
| | - Xiao Man Wu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Aquaculture Disease Control, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, 430072, China
| | - Yi Wei Hu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Aquaculture Disease Control, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, 430072, China
| |
Collapse
|
33
|
Sakai-Kawada FE, Ip CG, Hagiwara KA, Nguyen HYX, Yakym CJAV, Helmkampf M, Armstrong EE, Awaya JD. Characterization of Prodiginine Pathway in Marine Sponge-Associated Pseudoalteromonas sp. PPB1 in Hilo, Hawai‘i. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2020. [DOI: 10.3389/fsufs.2020.600201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Interest in bioactive pigments stems from their ecological role in adaptation, as well as their applications in various consumer products. The production of these bioactive pigments can be from a variety of biological sources, including simple microorganisms that may or may not be associated with a host. This study is particularly interested in the marine sponges, which have been known to harbor microorganisms that produce secondary metabolites like bioactive pigments. In this study, marine sponge tissue samples were collected from Puhi Bay off the Eastern shore of Hilo, Hawai‘i and subsequently were identified as Petrosia sp. with red pigmentation. Using surface sterilization and aseptic plating of sponge tissue samples, sponge-associated microorganisms were isolated. One isolate (PPB1) produced a colony with red pigmentation like that of Petrosia sp., suggesting an integral relationship between this particular isolate and the sponge of interest. 16S characterization and sequencing of PPB1 revealed that it belonged to the Pseudoalteromonas genus. Using various biological assays, both antimicrobial and antioxidant bioactivity was shown in Pseudoalteromonas sp. PPB1 crude extract. To further investigate the genetics of pigment production, a draft genome of PPB1 was sequenced, assembled, and annotated. This revealed a prodiginine biosynthetic pathway and the first cited-incidence of a prodiginine-producing Pseudoalteromonas species isolated from a marine sponge host. Further understanding into the bioactivity and biosynthesis of secondary metabolites like pigmented prodiginine may uncover the complex ecological interactions between host sponge and microorganism.
Collapse
|
34
|
de Oliveira BFR, Freitas-Silva J, Sánchez-Robinet C, Laport MS. Transmission of the sponge microbiome: moving towards a unified model. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:619-638. [PMID: 33048474 DOI: 10.1111/1758-2229.12896] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 10/08/2020] [Accepted: 10/11/2020] [Indexed: 06/11/2023]
Abstract
Sponges have co-evolved for millions of years alongside several types of microorganisms, which aside from participating in the animal's diet, are mostly symbionts. Since most of the genetic repertoire in the holobiont genome is provided by microbes, it is expected that the host-associated microbiome will be at least partially heritable. Sponges can therefore acquire their symbionts in different ways. Both vertical transmission (VT) and horizontal transmission (HT) have different advantages and disadvantages in the life cycle of these invertebrates. However, a third mode of transmission, called leaky vertical transmission or mixed mode of transmission (MMT), which incorporates both VT and HT modes, has gained relevance and seems to be the most robust model. In that regard, the aim of this review is to present the evolving knowledge on these main modes of transmission of the sponge microbiome. Our conclusions lead us to suggest that MMT may be more common for all sponges, with its frequency varying across the transmission spectrum between species and the environment. This hybrid model supports the stable and specific transmission of these microbial partners and reinforces their assistance in the resilience of sponges over the years.
Collapse
Affiliation(s)
- Bruno Francesco Rodrigues de Oliveira
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Cidade Universitária, 21941-590, Rio de Janeiro, Brazil
| | - Jéssyca Freitas-Silva
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Cidade Universitária, 21941-590, Rio de Janeiro, Brazil
| | - Claudia Sánchez-Robinet
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Cidade Universitária, 21941-590, Rio de Janeiro, Brazil
| | - Marinella Silva Laport
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Cidade Universitária, 21941-590, Rio de Janeiro, Brazil
| |
Collapse
|
35
|
Popkes M, Valenzano DR. Microbiota-host interactions shape ageing dynamics. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190596. [PMID: 32772667 PMCID: PMC7435156 DOI: 10.1098/rstb.2019.0596] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2020] [Indexed: 12/12/2022] Open
Abstract
Occupying the interface between host and environment, host-associated microbes play fundamental roles in nutrient absorption, essential metabolite synthesis, development of the immune system, defence against pathogens and pathogenesis. Microbiota composition and function is rather stable during adulthood, while it dramatically changes during early development, frailty and disease. Ageing is associated with progressive decrease of homeostasis, often resulting in disruption of the physiological balance between host and commensal microbes, ultimately leading to dysbiosis and host demise. Generally, high microbial diversity is associated with health and a youthful state, while low individual microbial diversity and larger inter-individual microbial diversity is associated with ageing and disease states. Different species are equipped with species-specific commensal, symbiotic and pathogenic microbial communities. How and whether the specific host-microbiota consortia co-evolved with host physiology to ensure homeostasis and promote individual fitness remains an open question. In this essay, we propose that the evolution of vertebrate-specific immune adaptations may have enabled the establishment of highly diverse, species-specific commensal microbial communities. We discuss how the maintenance of intact immune surveillance mechanisms, which allow discrimination between commensal and pathogenic bacteria, fail during ageing and lead to the onset of known ageing-related diseases. We discuss how host-microbiota interactions are key to maintaining homeostasis despite external perturbations, but also how they affect a range of host-specific ageing-related phenotypes. This article is part of the theme issue 'The role of the microbiome in host evolution'.
Collapse
Affiliation(s)
- Miriam Popkes
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Dario Riccardo Valenzano
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- CECAD, University of Cologne, Cologne, Germany
| |
Collapse
|
36
|
He R, Liu X, Zhang J, Wang Z, Wang W, Fu L, Fan Y, Sun S, Cao Y, Zhan L, Shui L. NLRC5 Inhibits Inflammation of Secretory Phase Ectopic Endometrial Stromal Cells by Up-Regulating Autophagy in Ovarian Endometriosis. Front Pharmacol 2020; 11:1281. [PMID: 33013364 PMCID: PMC7461939 DOI: 10.3389/fphar.2020.01281] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 08/03/2020] [Indexed: 01/20/2023] Open
Abstract
Nod-like receptor (NLR) family caspase activation and recruitment domain containing 5 (NLRC5) is a newly identified sub-class of the NLR family. It regulates inflammation and has a key function in innate and adaptive immunologic reactions. Autophagy has been reported to be crucially linked to the pathogenesis of endometriosis. Our recent study identify there is a negative correlation between NLRC5 and autophagy in endometriosis, indicating that NLRC5 and autophagy together act as promising predictors in endometriosis patients. However, the mechanism associating NLRC5 and autophagy in endometriosis is still not completely understood. We hypothesize that autophagy could be involved in NLRC5-mediated inflammation in endometriosis. In order to validate the assumption, we evaluate the effects of NLRC5 and autophagy in the inflammation of ectopic endometrial stromal cells (EESCs) of ovarian endometriosis patients, to specifically determine whether autophagy is involved in NLRC5-mediated inflammation in EESCs. Our results show that over-expression of NLRC5 results in the up-regulation of autophagy in EESCs and inhibition of NLRC5 restricts the level of autophagy in EESCs. Furthermore, over-expression of NLRC5 and promotion of autophagy inhibit interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α) expressions, whereas inhibition of NLRC5 and autophagy up-regulate IL-6 and TNF-α expressions in EESCs. Additionally, promotion of autophagy contributes to the NLRC5-mediated inhibition of IL-6 and TNF-α expressions in EESCs; inhibition of autophagy restricts NLRC5-mediated inhibition of IL-6 and TNF-α expressions in EESCs. Our results suggest that over-expression of NLRC5 promotes autophagy, thereby inhibiting inflammation in ovarian endometriosis.
Collapse
Affiliation(s)
- Runhua He
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Xiaojing Liu
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Jing Zhang
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Zhongzheng Wang
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Wenyan Wang
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Liutao Fu
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yijun Fan
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Shiying Sun
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yunxia Cao
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Lei Zhan
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.,Reproductive Medicine Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Lijun Shui
- Clinical Center of Reproductive Medicine, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China
| |
Collapse
|
37
|
Dierking K, Pita L. Receptors Mediating Host-Microbiota Communication in the Metaorganism: The Invertebrate Perspective. Front Immunol 2020; 11:1251. [PMID: 32612612 PMCID: PMC7308585 DOI: 10.3389/fimmu.2020.01251] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/18/2020] [Indexed: 11/23/2022] Open
Abstract
Multicellular organisms live in close association with a plethora of microorganism, which have a profound effect on multiple host functions. As such, the microbiota and its host form an intimate functional entity, termed the metaorganism or holobiont. But how does the metaorganism communicate? Which receptors recognize microbial signals, mediate the effect of the microbiota on host physiology or regulate microbiota composition and homeostasis? In this review we provide an overview on the function of different receptor classes in animal host-microbiota communication. We put a special focus on invertebrate hosts, including both traditional invertebrate models such as Drosophila melanogaster and Caenorhabditis elegans and “non-model” invertebrates in microbiota research. Finally, we highlight the potential of invertebrate systems in studying mechanism of host-microbiota interactions.
Collapse
Affiliation(s)
- Katja Dierking
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Lucía Pita
- RD3 Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| |
Collapse
|
38
|
Traylor-Knowles N, Vandepas LE, Browne WE. Still Enigmatic: Innate Immunity in the Ctenophore Mnemiopsis leidyi. Integr Comp Biol 2020; 59:811-818. [PMID: 31251332 DOI: 10.1093/icb/icz116] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Innate immunity is an ancient physiological response critical for protecting metazoans from invading pathogens. It is the primary pathogen defense mechanism among invertebrates. While innate immunity has been studied extensively in diverse invertebrate taxa, including mollusks, crustaceans, and cnidarians, this system has not been well characterized in ctenophores. The ctenophores comprise an exclusively marine, non-bilaterian lineage that diverged early during metazoan diversification. The phylogenetic position of ctenophore lineage suggests that characterization of the ctenophore innate immune system will reveal important features associated with the early evolution of the metazoan innate immune system. Here, we review current understanding of the ctenophore immune repertoire and identify innate immunity genes recovered from three ctenophore species. We also isolate and characterize Mnemiopsis leidyi cells that display macrophage-like behavior when challenged with bacteria. Our results indicate that ctenophores possess cells capable of phagocytosing microbes and that two distantly related ctenophores, M. leidyi and Hormiphora californiensis, possess many candidate innate immunity proteins.
Collapse
Affiliation(s)
- Nikki Traylor-Knowles
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, FL 33149, USA
| | - Lauren E Vandepas
- Benaroya Research Institute, 1201 9th Avenue, Seattle, WA 98101, USA.,Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - William E Browne
- Department of Biology, University of Miami, Cox Science Building, 1301 Memorial Drive, Miami, FL 33146, USA
| |
Collapse
|
39
|
McCord JP, Grove TZ. Engineering repeat proteins of the immune system. Biopolymers 2020; 111:e23348. [PMID: 32031681 DOI: 10.1002/bip.23348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 08/30/2019] [Accepted: 09/06/2019] [Indexed: 11/06/2022]
Abstract
Limitations associated with immunoglobulins have motivated the search for novel binding scaffolds. Repeat proteins have emerged as one promising class of scaffolds, but often are limited to binding protein and peptide targets. An exception is the repeat proteins of the immune system, which have in recent years served as an inspiration for binding scaffolds which can bind glycans and other classes of biomolecule. Like other repeat proteins, these proteins can be very stable and have a monomeric mode of binding, with elongated and highly variable binding surfaces. The ability to target glycans and glycoproteins fill an important gap in current tools for research and biomedical applications.
Collapse
Affiliation(s)
- Jennifer P McCord
- Department of Chemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, U.S.A
| | - Tijana Z Grove
- Department of Chemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, U.S.A.,Zarkovic Grove Consulting, LLC, Blacksburg, VA, U.S.A
| |
Collapse
|
40
|
Leach WB, Carrier TJ, Reitzel AM. Diel patterning in the bacterial community associated with the sea anemone Nematostella vectensis. Ecol Evol 2019; 9:9935-9947. [PMID: 31534705 PMCID: PMC6745676 DOI: 10.1002/ece3.5534] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/11/2019] [Accepted: 07/22/2019] [Indexed: 12/12/2022] Open
Abstract
Microbes can play an important role in the physiology of animals by providing essential nutrients, inducing immune pathways, and influencing the specific species that compose the microbiome through competitive or facilitatory interactions. The community of microbes associated with animals can be dynamic depending on the local environment, and factors that influence the composition of the microbiome are essential to our understanding of how microbes may influence the biology of their animal hosts. Regularly repeated changes in the environment, such as diel lighting, can result in two different organismal responses: a direct response to the presence and absence of exogenous light and endogenous rhythms resulting from a molecular circadian clock, both of which can influence the associated microbiota. Here, we report how diel lighting and a potential circadian clock impacts the diversity and relative abundance of bacteria in the model cnidarian Nematostella vectensis using an amplicon-based sequencing approach. Comparisons of bacterial communities associated with anemones cultured in constant darkness and in light:dark conditions revealed that individuals entrained in the dark had a more diverse microbiota. Overall community composition showed little variation over a 24-hr period in either treatment; however, abundances of individual bacterial OTUs showed significant cycling in each treatment. A comparative analysis of genes involved in the innate immune system of cnidarians showed differential expression between lighting conditions in N. vectensis, with significant up-regulation during long-term darkness for a subset of genes. Together, our studies support a hypothesis that the bacterial community associated with this species is relatively stable under diel light conditions when compared with static conditions and that particular bacterial members may have time-dependent abundance that coincides with the diel photoperiod in an otherwise stable community.
Collapse
Affiliation(s)
- Whitney B. Leach
- Department of Biological SciencesUniversity of North Carolina at CharlotteCharlotteNCUSA
| | - Tyler J. Carrier
- Department of Biological SciencesUniversity of North Carolina at CharlotteCharlotteNCUSA
| | - Adam M. Reitzel
- Department of Biological SciencesUniversity of North Carolina at CharlotteCharlotteNCUSA
| |
Collapse
|
41
|
Chen J, Shang S, Wu X, Zhong H, Zhao C, Wei Q, Zhang H, Xia T, Chen Y, Zhang H, Tang X. Genomic analysis and adaptive evolution of the RIG-I-like and NOD-like receptors in reptiles. Int J Biol Macromol 2019; 134:1045-1051. [DOI: 10.1016/j.ijbiomac.2019.05.172] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 05/21/2019] [Accepted: 05/22/2019] [Indexed: 12/24/2022]
|
42
|
Vertical transmission of sponge microbiota is inconsistent and unfaithful. Nat Ecol Evol 2019; 3:1172-1183. [PMID: 31285574 DOI: 10.1038/s41559-019-0935-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 05/29/2019] [Indexed: 01/18/2023]
Abstract
Co-evolutionary theory predicts that if beneficial microbial symbionts improve host fitness, they should be faithfully transmitted to offspring. More recently, the hologenome theory of evolution predicts resemblance between parent and offspring microbiomes and high partner fidelity between host species and their vertically transmitted microbes. Here, we test these ideas in multiple coexisting host species with highly diverse microbiota, leveraging known parent-offspring pairs sampled from eight species of wild marine sponges (Porifera). We found that the processes governing vertical transmission were both neutral and selective. A neutral model was a better fit to larval (R2 = 0.66) than to the adult microbiota (R2 = 0.27), suggesting that the importance of non-neutral processes increases as the sponge host matures. Microbes that are enriched above neutral expectations in adults were disproportionately transferred to offspring. Patterns of vertical transmission were, however, incomplete: larval sponges shared, on average, 44.8% of microbes with their parents, which was not higher than the fraction they shared with nearby non-parental adults. Vertical transmission was also inconsistent across siblings, as larval sponges from the same parent shared only 17% of microbes. Finally, we found no evidence that vertically transmitted microbes are faithful to a single sponge host species. Surprisingly, larvae were as likely to share vertically transmitted microbes with larvae from other sponge species as they were with their own species. Our study demonstrates that common predictions of vertical transmission that stem from species-poor systems are not necessarily true when scaling up to diverse and complex microbiomes.
Collapse
|
43
|
Comparative study on pattern recognition receptors in non-teleost ray-finned fishes and their evolutionary significance in primitive vertebrates. SCIENCE CHINA-LIFE SCIENCES 2019; 62:566-578. [PMID: 30929190 DOI: 10.1007/s11427-019-9481-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 11/28/2018] [Indexed: 12/11/2022]
Abstract
Pattern recognition receptors (PRRs) play important roles in innate immunity system and trigger the specific pathogen recognition by detecting the pathogen-associated molecular patterns. The main four PRRs components including Toll-like receptors (TLRs), RIG-I-like receptors (RLRs), NOD-like receptors (NLRs) and C-type lectin receptors (CLRs) were surveyed in the five genomes of non-teleost ray-finned fishes (NTR) including bichir (Polypterus senegalus), American paddlefish (Polyodon spathula), alligator gar (Atractosteus spatula), spotted gar (Lepisosteus oculatus) and bowfin (Amia calva), representing all the four major basal groups of ray-finned fishes. The result indicates that all the four PRRs components have been well established in these NTR fishes. In the RLR-MAVS signal pathway, which detects intracellular RNA ligands to induce production of type I interferons (IFNs), the MAVS was lost in bichir particularly. Also, the essential genes of recognition of Lipopolysaccharide (LPS) commonly in mammals like MD2, LY96 and LBP could not be identified in NTR fishes. It is speculated that TLR4 in NTR fishes may act as a cooperator with other PRRs and has a different pathway of recognizing LPS compared with that in mammals. In addition, we provide a survey of NLR and CLR in NTR fishes. The CLRs results suggest that Group V receptors are absent in fishes and Group II and VI receptors are well established in the early vertebrate evolution. Our comprehensive research of PRRs involving NTR fishes provides a new insight into PRR evolution in primitive vertebrate.
Collapse
|
44
|
Pita L, Hoeppner MP, Ribes M, Hentschel U. Differential expression of immune receptors in two marine sponges upon exposure to microbial-associated molecular patterns. Sci Rep 2018; 8:16081. [PMID: 30382170 PMCID: PMC6208332 DOI: 10.1038/s41598-018-34330-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Accepted: 10/12/2018] [Indexed: 02/07/2023] Open
Abstract
The innate immune system helps animals to navigate the microbial world. The response to microbes relies on the specific recognition of microbial-associated molecular patterns (MAMPs) by immune receptors. Sponges (phylum Porifera), as early-diverging animals, provide insights into conserved mechanisms for animal-microbe crosstalk. However, experimental data is limited. We adopted an experimental approach followed by RNA-Seq and differential gene expression analysis in order to characterise the sponge immune response. Two Mediterranean species, Aplysina aerophoba and Dysidea avara, were exposed to a “cocktail” of MAMPs (lipopolysaccharide and peptidoglycan) or to sterile artificial seawater (control) and sampled 1 h, 3 h, and 5 h post-treatment for RNA-Seq. The response involved, first and foremost, a higher number of differentially-expressed genes in A. aerophoba than D. avara. Secondly, while both species constitutively express a diverse repertoire of immune receptors, they differed in their expression profiles upon MAMP challenge. The response in D. avara was mediated by increased expression of two NLR genes, whereas the response in A. aerophoba involved SRCR and GPCR genes. From the set of annotated genes we infer that both species activated apoptosis in response to MAMPs while in A. aerophoba phagocytosis was additionally stimulated. Our study assessed for the first time the transcriptomic responses of sponges to MAMPs and revealed conserved and species-specific features of poriferan immunity as well as genes potentially relevant to animal-microbe interactions.
Collapse
Affiliation(s)
- Lucía Pita
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany.
| | - Marc P Hoeppner
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Germany
| | - Marta Ribes
- Institute of Marine Science, CSIC, Barcelona, Spain
| | - Ute Hentschel
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany.,Christian-Albrechts-University of Kiel (CAU), Kiel, Germany
| |
Collapse
|
45
|
Richter DJ, Fozouni P, Eisen MB, King N. Gene family innovation, conservation and loss on the animal stem lineage. eLife 2018; 7:34226. [PMID: 29848444 PMCID: PMC6040629 DOI: 10.7554/elife.34226] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 05/26/2018] [Indexed: 02/06/2023] Open
Abstract
Choanoflagellates, the closest living relatives of animals, can provide unique insights into the changes in gene content that preceded the origin of animals. However, only two choanoflagellate genomes are currently available, providing poor coverage of their diversity. We sequenced transcriptomes of 19 additional choanoflagellate species to produce a comprehensive reconstruction of the gains and losses that shaped the ancestral animal gene repertoire. We identified ~1944 gene families that originated on the animal stem lineage, of which only 39 are conserved across all animals in our study. In addition, ~372 gene families previously thought to be animal-specific, including Notch, Delta, and homologs of the animal Toll-like receptor genes, instead evolved prior to the animal-choanoflagellate divergence. Our findings contribute to an increasingly detailed portrait of the gene families that defined the biology of the Urmetazoan and that may underpin core features of extant animals. All animals, from sea sponges and reef-building corals to elephants and humans, share a single common ancestor that lived over half a billion years ago. This single-celled predecessor evolved the ability to develop into a creature made up of many cells with specialized jobs. Reconstructing the steps in this evolutionary process has been difficult because the earliest animals were soft-bodied and microscopic and did not leave behind fossils that scientists can study. Though their bodies have since disintegrated, many of the instructions for building the first animals live on in genes that were passed on to life forms that still exist. Scientists are trying to retrace those genes back to the first animal by comparing the genomes of living animals with their closest relatives, the choanoflagellates. Choanoflagellates are single-celled, colony-forming organisms that live in waters around the world. Comparisons with choanoflagellates may help scientists identify which genes were necessary to help animals evolve and diversify into so many different species. So far, 1,000 animal and two choanoflagellate genomes have been sequenced. But the gene repertoires of most species of choanoflagellates have yet to be analyzed. Now, Richter et al. have cataloged the genes of 19 more species of choanoflagellates. This added information allowed them to recreate the likely gene set of the first animal and to identify genetic changes that occurred during animal evolution. The analyses showed that modern animals lost about a quarter of the genes present in their last common ancestor with choanoflagellates and gained an equal number of new genes. Richter et al. identified several dozen core animal genes that were gained and subsequently preserved throughout animal evolution. Many of these are necessary so that an embryo can develop properly, but the precise roles of some core genes remain a mystery. Most other genes that emerged in the first animals have been lost in at least one living animal. The study of Richter et al. also showed that some very important genes in animals, including genes essential for early development and genes that help the immune system detect pathogens, predate animals. These key genes trace back to animals’ last common ancestor with choanoflagellates and may have evolved new roles in animals.
Collapse
Affiliation(s)
- Daniel J Richter
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States.,Sorbonne Universités, UPMC Univ Paris 06, CNRS UMR 7144, Adaptation et Diversité en Milieu Marin, Équipe EPEP, Station Biologique de Roscoff, Roscoff, France
| | - Parinaz Fozouni
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States.,Medical Scientist Training Program, Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, United States.,Gladstone Institutes, San Francisco, United States
| | - Michael B Eisen
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - Nicole King
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| |
Collapse
|
46
|
Gaiti F, Hatleberg WL, Tanurdžić M, Degnan BM. Sponge Long Non-Coding RNAs Are Expressed in Specific Cell Types and Conserved Networks. Noncoding RNA 2018; 4:ncrna4010006. [PMID: 29657303 PMCID: PMC5890393 DOI: 10.3390/ncrna4010006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 02/05/2018] [Accepted: 02/27/2018] [Indexed: 02/06/2023] Open
Abstract
Although developmental regulation by long non-coding RNAs (lncRNAs) appears to be a widespread feature amongst animals, the origin and level of evolutionary conservation of this mode of regulation remain unclear. We have previously demonstrated that the sponge Amphimedon queenslandica—a morphologically-simple animal—developmentally expresses an array of lncRNAs in manner akin to more complex bilaterians (insects + vertebrates). Here, we first show that Amphimedon lncRNAs are expressed in specific cell types in larvae, juveniles and adults. Thus, as in bilaterians, sponge developmental regulation involves the dynamic, cell type- and context-specific regulation of specific lncRNAs. Second, by comparing gene co-expression networks between Amphimedon queenslandica and Sycon ciliatum—a distantly-related calcisponge—we identify several putative co-expression modules that appear to be shared in sponges; these network-embedded sponge lncRNAs have no discernable sequence similarity. Together, these results suggest sponge lncRNAs are developmentally regulated and operate in conserved gene regulatory networks, as appears to be the case in more complex bilaterians.
Collapse
Affiliation(s)
- Federico Gaiti
- School of Biological Sciences, University of Queensland, Brisbane, QLD 4072, Australia.
- Department of Medicine, Weill Cornell Medicine, and New York Genome Center, New York, NY 10021, USA.
| | - William L Hatleberg
- School of Biological Sciences, University of Queensland, Brisbane, QLD 4072, Australia.
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
| | - Miloš Tanurdžić
- School of Biological Sciences, University of Queensland, Brisbane, QLD 4072, Australia.
| | - Bernard M Degnan
- School of Biological Sciences, University of Queensland, Brisbane, QLD 4072, Australia.
| |
Collapse
|
47
|
Activation of the Innate Immune Receptors: Guardians of the Micro Galaxy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1024:1-35. [DOI: 10.1007/978-981-10-5987-2_1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
48
|
Meunier E, Broz P. Evolutionary Convergence and Divergence in NLR Function and Structure. Trends Immunol 2017; 38:744-757. [PMID: 28579324 DOI: 10.1016/j.it.2017.04.005] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 04/13/2017] [Accepted: 04/21/2017] [Indexed: 12/11/2022]
Abstract
The recognition of cellular damage caused by either pathogens or abiotic stress is essential for host defense in all forms of life in the plant and animal kingdoms. The NOD-like receptors (NLRs) represent a large family of multidomain proteins that were initially discovered for their role in host defense in plants and vertebrates. Over recent years the wide distribution of NLRs among metazoans has become apparent and their origins have begun to emerge. Moreover, intense study of NLR function has shown that they play essential roles beyond pathogen recognition - in the regulation of antigen presentation, cell death, inflammation, and even in embryonic development. We summarize here the latest insights into NLR biology and discuss examples of converging and diverging evolution of NLR function and structure.
Collapse
Affiliation(s)
- Etienne Meunier
- Focal Area Infection Biology, Biozentrum, University of Basel, 4056 Basel, Switzerland; Institute of Pharmacology and Structural Biology (IPBS), University of Toulouse, France
| | - Petr Broz
- Focal Area Infection Biology, Biozentrum, University of Basel, 4056 Basel, Switzerland.
| |
Collapse
|
49
|
Bentham A, Burdett H, Anderson PA, Williams SJ, Kobe B. Animal NLRs provide structural insights into plant NLR function. ANNALS OF BOTANY 2017; 119:827-702. [PMID: 27562749 PMCID: PMC5378188 DOI: 10.1093/aob/mcw171] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 05/26/2016] [Accepted: 06/07/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND The plant immune system employs intracellular NLRs (nucleotide binding [NB], leucine-rich repeat [LRR]/nucleotide-binding oligomerization domain [NOD]-like receptors) to detect effector proteins secreted into the plant cell by potential pathogens. Activated plant NLRs trigger a range of immune responses, collectively known as the hypersensitive response (HR), which culminates in death of the infected cell. Plant NLRs show structural and functional resemblance to animal NLRs involved in inflammatory and innate immune responses. Therefore, knowledge of the activation and regulation of animal NLRs can help us understand the mechanism of action of plant NLRs, and vice versa. SCOPE This review provides an overview of the innate immune pathways in plants and animals, focusing on the available structural and biochemical information available for both plant and animal NLRs. We highlight the gap in knowledge between the animal and plant systems, in particular the lack of structural information for plant NLRs, with crystal structures only available for the N-terminal domains of plant NLRs and an integrated decoy domain, in contrast to the more complete structures available for animal NLRs. We assess the similarities and differences between plant and animal NLRs, and use the structural information on the animal NLR pair NAIP/NLRC4 to derive a plausible model for plant NLR activation. CONCLUSIONS Signalling by cooperative assembly formation (SCAF) appears to operate in most innate immunity pathways, including plant and animal NLRs. Our proposed model of plant NLR activation includes three key steps: (1) initially, the NLR exists in an inactive auto-inhibited state; (2) a combination of binding by activating elicitor and ATP leads to a structural rearrangement of the NLR; and (3) signalling occurs through cooperative assembly of the resistosome. Further studies, structural and biochemical in particular, will be required to provide additional evidence for the different features of this model and shed light on the many existing variations, e.g. helper NLRs and NLRs containing integrated decoys.
Collapse
Affiliation(s)
- Adam Bentham
- School of Biological Sciences, Flinders University, Adelaide, SA 5001, Australia
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Hayden Burdett
- School of Biological Sciences, Flinders University, Adelaide, SA 5001, Australia
| | - Peter A. Anderson
- School of Biological Sciences, Flinders University, Adelaide, SA 5001, Australia
| | - Simon J. Williams
- School of Biological Sciences, Flinders University, Adelaide, SA 5001, Australia
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland 4072, Australia
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra 2601, Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland 4072, Australia
- For correspondence. E-mail
| |
Collapse
|
50
|
The NBS-LRR architectures of plant R-proteins and metazoan NLRs evolved in independent events. Proc Natl Acad Sci U S A 2017; 114:1063-1068. [PMID: 28096345 PMCID: PMC5293065 DOI: 10.1073/pnas.1619730114] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
There are intriguing parallels between plants and animals, with respect to the structures of their innate immune receptors, that suggest universal principles of innate immunity. The cytosolic nucleotide binding site-leucine rich repeat (NBS-LRR) resistance proteins of plants (R-proteins) and the so-called NOD-like receptors of animals (NLRs) share a domain architecture that includes a STAND (signal transduction ATPases with numerous domains) family NTPase followed by a series of LRRs, suggesting inheritance from a common ancestor with that architecture. Focusing on the STAND NTPases of plant R-proteins, animal NLRs, and their homologs that represent the NB-ARC (nucleotide-binding adaptor shared by APAF-1, certain R gene products and CED-4) and NACHT (named for NAIP, CIIA, HET-E, and TEP1) subfamilies of the STAND NTPases, we analyzed the phylogenetic distribution of the NBS-LRR domain architecture, used maximum-likelihood methods to infer a phylogeny of the NTPase domains of R-proteins, and reconstructed the domain structure of the protein containing the common ancestor of the STAND NTPase domain of R-proteins and NLRs. Our analyses reject monophyly of plant R-proteins and NLRs and suggest that the protein containing the last common ancestor of the STAND NTPases of plant R-proteins and animal NLRs (and, by extension, all NB-ARC and NACHT domains) possessed a domain structure that included a STAND NTPase paired with a series of tetratricopeptide repeats. These analyses reject the hypothesis that the domain architecture of R-proteins and NLRs was inherited from a common ancestor and instead suggest the domain architecture evolved at least twice. It remains unclear whether the NBS-LRR architectures were innovations of plants and animals themselves or were acquired by one or both lineages through horizontal gene transfer.
Collapse
|