1
|
Wei M, Qin Z, Kong D, Liu D, Zheng Q, Bai S, Zhang Z, Ma Y. Echiuran Hox genes provide new insights into the correspondence between Hox subcluster organization and collinearity pattern. Proc Biol Sci 2022; 289:20220705. [PMID: 36264643 PMCID: PMC9449475 DOI: 10.1098/rspb.2022.0705] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 07/29/2022] [Indexed: 09/16/2023] Open
Abstract
In many bilaterians, Hox genes are generally clustered along the chromosomes and expressed in spatial and temporal order. In vertebrates, the expression of Hox genes follows a whole-cluster spatio-temporal collinearity (WSTC) pattern, whereas in some invertebrates the expression of Hox genes exhibits a subcluster-level spatio-temporal collinearity pattern. In bilaterians, the diversity of collinearity patterns and the cause of collinearity differences in Hox gene expression remain poorly understood. Here, we investigate genomic organization and expression pattern of Hox genes in the echiuran worm Urechis unicinctus (Annelida, Echiura). Urechis unicinctus has a split cluster with four subclusters divided by non-Hox genes: first subcluster (Hox1 and Hox2), second subcluster (Hox3), third subcluster (Hox4, Hox5, Lox5, Antp and Lox4), fourth subcluster (Lox2 and Post2). The expression of U. unicinctus Hox genes shows a subcluster-based whole-cluster spatio-temporal collinearity (S-WSTC) pattern: the anterior-most genes in each subcluster are activated in a spatially and temporally colinear manner (reminiscent of WSTC), with the subsequent genes in each subcluster then being very similar to their respective anterior-most subcluster gene. Combining genomic organization and expression profiles of Hox genes in different invertebrate lineages, we propose that the spatio-temporal collinearity of invertebrate Hox is subcluster-based.
Collapse
Affiliation(s)
- Maokai Wei
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Zhenkui Qin
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Dexu Kong
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Danwen Liu
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Qiaojun Zheng
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Shumiao Bai
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Zhifeng Zhang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, People's Republic of China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, People's Republic of China
| | - Yubin Ma
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, People's Republic of China
| |
Collapse
|
2
|
de la Ballina NR, Maresca F, Cao A, Villalba A. Bivalve Haemocyte Subpopulations: A Review. Front Immunol 2022; 13:826255. [PMID: 35464425 PMCID: PMC9024128 DOI: 10.3389/fimmu.2022.826255] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/23/2022] [Indexed: 12/26/2022] Open
Abstract
Bivalve molluscs stand out for their ecological success and their key role in the functioning of aquatic ecosystems, while also constituting a very valuable commercial resource. Both ecological success and production of bivalves depend on their effective immune defence function, in which haemocytes play a central role acting as both the undertaker of the cellular immunity and supplier of the humoral immunity. Bivalves have different types of haemocytes, which perform different functions. Hence, identification of cell subpopulations and their functional characterisation in immune responses is essential to fully understand the immune system in bivalves. Nowadays, there is not a unified nomenclature that applies to all bivalves. Characterisation of bivalve haemocyte subpopulations is often combined with 1) other multiple parameter assays to determine differences between cell types in immune-related physiological activities, such as phagocytosis, oxidative stress and apoptosis; and 2) immune response to different stressors such as pathogens, temperature, acidification and pollution. This review summarises the major and most recent findings in classification and functional characterisation of the main haemocyte types of bivalve molluscs.
Collapse
Affiliation(s)
- Nuria R. de la Ballina
- Centro de Investigacións Mariñas (CIMA), Consellería do Mar, Xunta de Galicia, Vilanova de Arousa, Spain
| | - Francesco Maresca
- MARE - Marine and Environmental Sciences Centre, Laboratório de Ciências do Mar, Universidade de Évora, Sines, Portugal
| | - Asunción Cao
- Centro de Investigacións Mariñas (CIMA), Consellería do Mar, Xunta de Galicia, Vilanova de Arousa, Spain
| | - Antonio Villalba
- Centro de Investigacións Mariñas (CIMA), Consellería do Mar, Xunta de Galicia, Vilanova de Arousa, Spain
- Departamento de Ciencias de la Vida, Universidad de Alcalá, Alcalá de Henares, Spain
- Research Centre for Experimental Marine Biology and Biotechnology, Plentziako Itsas Estazioa (PIE), University of the Basque Country (UPV/EHU), Plentzia, Spain
- *Correspondence: Antonio Villalba,
| |
Collapse
|
3
|
Campos DA, Pereira EC, Jardim R, Cuadrat RRC, Bernardes JS, Dávila AMR. Homology Inference Based on a Reconciliation Approach for the Comparative Genomics of Protozoa. Evol Bioinform Online 2018; 14:1176934318785138. [PMID: 30034216 PMCID: PMC6048835 DOI: 10.1177/1176934318785138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 05/30/2018] [Indexed: 11/16/2022] Open
Abstract
Protozoa parasites are responsible for several diseases in tropical countries, such as malaria, sleeping sickness, Chagas disease, leishmaniasis, amebiasis, and giardiasis, which together threaten millions of people around the world. In addition, most of the classic parasitic diseases due to protozoa are zoonotic. Understanding the biology of these organisms plays a relevant role in combating these diseases. Using homology inference and comparative genomics, this study targeted 3 protozoan species from different Phyla: Cryptosporidium muris (Apicomplexa), Entamoeba invadens (Amoebozoa), and Trypanosoma grayi (Euglenozoa). In this study, we propose a new approach for the identification of homologs, based on the reconciliation of the results of 2 different homology inference software programs. Our results showed that 46.1% (59/128) of the groups inferred by our reconciliation approach could be validated using this methodology. These validated groups are here called homologous Supergroups and were compared with SUPERFAMILY and Pfam Clans.
Collapse
Affiliation(s)
- Darueck A Campos
- Acre Federal Institute of Education,
Science and Technology, Rio Branco, Brazil
- Computational and Systems Biology
Laboratory, Oswaldo Cruz Institute (FIOCRUZ), Rio de Janeiro, Brazil
| | - Elisa C Pereira
- Computational and Systems Biology
Laboratory, Oswaldo Cruz Institute (FIOCRUZ), Rio de Janeiro, Brazil
| | - Rodrigo Jardim
- Computational and Systems Biology
Laboratory, Oswaldo Cruz Institute (FIOCRUZ), Rio de Janeiro, Brazil
| | - Rafael RC Cuadrat
- Computational and Systems Biology
Laboratory, Oswaldo Cruz Institute (FIOCRUZ), Rio de Janeiro, Brazil
- Bioinformatics core facility, Max Planck
Institute for Biology of Ageing, Cologne, Germany
| | - Juliana S Bernardes
- Biologie Computationnelle et
Quantitative, Université Pierre et Marie Curie, Paris, France
| | - Alberto MR Dávila
- Computational and Systems Biology
Laboratory, Oswaldo Cruz Institute (FIOCRUZ), Rio de Janeiro, Brazil
| |
Collapse
|
4
|
Xu Z, Regenstein JM, Xie D, Lu W, Ren X, Yuan J, Mao L. The oxidative stress and antioxidant responses of Litopenaeus vannamei to low temperature and air exposure. FISH & SHELLFISH IMMUNOLOGY 2018; 72:564-571. [PMID: 29133253 DOI: 10.1016/j.fsi.2017.11.016] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 11/07/2017] [Accepted: 11/09/2017] [Indexed: 06/07/2023]
Abstract
Low temperature and air exposure were the key attributes for waterless transportation of fish and shrimp. In order to investigate the oxidative stress and antioxidant responses of the live shrimp Litopenaeus vannamei in the mimic waterless transportation, live shrimp were cooled at 13 °C for 3 min, stored in oxygen at 15 °C for 12 h, and then revived in water at 25 °C. The survival rate of shrimp under this waterless transportation system was over 86.67%. The ultrastructure of hepatopancreas cells were observed while activities of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), glutathione peroxidase (GSH-Px), antisuperoxide anion free radicals (ASAFR), total antioxidant capacity (TAOC), reactive oxygen species (ROS) production, content of malondialdehyde (MDA) and relative mRNA expressions of CAT and GSH-Px in the hemolymph and hepatopancreas were determined. Slight distortions of some organelles in hepatopancreas cells was reversible upon the shrimp revived from the cold shock. The activities of SOD, POD, CAT, GSH-Px, TAOC, ROS production and relative mRNA expressions of CAT and GSH-Px increased following the cold shock and reached peak levels after 3 or 6 h of storage, and then decreased gradually. There was no significant difference between the fresh and the revived shrimp in SOD, POD, GSH-Px, TAOC, ROS, MDA and relative mRNA expressions of CAT and GSH-Px. The oxidative stress and antioxidant responses were tissue-specific because hepatopancreas seemed to have a greater ability to defend against organelle damage and was more sensitive to stress than hemolymph based on the results of SOD activity, MDA content and GSH-Px mRNA expression. These results revealed that low temperature and air exposure caused significant oxidative and antioxidant responses, but did not lead to irreversible damages in this waterless system.
Collapse
Affiliation(s)
- Zihan Xu
- College of Biosystems Engineering and Food Science, Fuli Institute of Food Science, Zhejiang Key Laboratory of Agro-Food Processing, Zhejiang University, 310058, Hangzhou, Zhejiang, China; Department of Food Science, Cornell University, 14853-7201, Ithaca, NY, USA
| | - Joe M Regenstein
- Department of Food Science, Cornell University, 14853-7201, Ithaca, NY, USA
| | - Dandan Xie
- College of Biosystems Engineering and Food Science, Fuli Institute of Food Science, Zhejiang Key Laboratory of Agro-Food Processing, Zhejiang University, 310058, Hangzhou, Zhejiang, China
| | - Wenjing Lu
- College of Biosystems Engineering and Food Science, Fuli Institute of Food Science, Zhejiang Key Laboratory of Agro-Food Processing, Zhejiang University, 310058, Hangzhou, Zhejiang, China
| | - Xingchen Ren
- College of Biosystems Engineering and Food Science, Fuli Institute of Food Science, Zhejiang Key Laboratory of Agro-Food Processing, Zhejiang University, 310058, Hangzhou, Zhejiang, China
| | - Jiajia Yuan
- College of Biosystems Engineering and Food Science, Fuli Institute of Food Science, Zhejiang Key Laboratory of Agro-Food Processing, Zhejiang University, 310058, Hangzhou, Zhejiang, China
| | - Linchun Mao
- College of Biosystems Engineering and Food Science, Fuli Institute of Food Science, Zhejiang Key Laboratory of Agro-Food Processing, Zhejiang University, 310058, Hangzhou, Zhejiang, China.
| |
Collapse
|
5
|
López Y, Cepas V, Soto SM. The Marine Ecosystem as a Source of Antibiotics. GRAND CHALLENGES IN MARINE BIOTECHNOLOGY 2018. [DOI: 10.1007/978-3-319-69075-9_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
|