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Lang D, Wang X, Liu C, Geng W, Irwin DM, Chen S, Li C, Yu L, Xiao H. Birth-and-death evolution of ribonuclease 9 genes in Cetartiodactyla. SCIENCE CHINA LIFE SCIENCES 2022; 66:1170-1182. [PMID: 36443512 DOI: 10.1007/s11427-022-2195-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 08/30/2022] [Indexed: 11/30/2022]
Abstract
RNase9 plays a reproductive function and has been recognized as an important member of the ribonuclease (RNase) A superfamily, a gene family that is widely used as a model for molecular evolutionary studies. Here, we identified 178 RNase9 genes from 95 Cetartiodactyla species that represent all four lineages and 21 families of this clade. Unexpectedly, RNase9 experienced an evolutionary scenario of "birth and death" in Ruminantia, and expression analyses showed that duplicated RNase9A and RNase9B genes are expressed in reproductive tissues (epididymis, vas deferens or prostate). This expression pattern combined with the estimate that these genes duplicated during the middle Eocene, a time when Ruminantia become a successful lineage, suggests that the RNase9 gene duplication might have been advantageous for promoting sperm motility and male fertility as an adaptation to climate seasonality changes of this period. In contrast, all RNase9 genes were lost in the Cetacean lineage, which might be associated with their high levels of prostatic lesions and lower reproductive rates as adaptations to a fully aquatic environment and a balance to the demands of ocean resources. This study reveals a complex and intriguing evolutionary history and functional divergence for RNase9 in Cetartiodactyla, providing new insights into the evolution of the RNaseA superfamily and molecular mechanisms for organismal adaptations to the environment.
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Affiliation(s)
- Datian Lang
- School of Life Sciences, Yunnan University, Kunming, 650500, China
- Biodiversity Research Center of Wumeng Mountain, Department of Agronomy and Life Science, Zhaotong University, Zhaotong, 657000, China
| | - Xiaoping Wang
- School of Life Sciences, Yunnan University, Kunming, 650500, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, China
| | - Chunbing Liu
- School of Life Sciences, Yunnan University, Kunming, 650500, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, China
| | - Weihang Geng
- School of Life Sciences, Yunnan University, Kunming, 650500, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, China
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Shanyuan Chen
- School of Ecology and Environmental Science, Yunnan University, Kunming, 650091, China
| | - Chunqing Li
- School of Ecology and Environmental Science, Yunnan University, Kunming, 650091, China
| | - Li Yu
- School of Life Sciences, Yunnan University, Kunming, 650500, China.
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, China.
| | - Heng Xiao
- School of Life Sciences, Yunnan University, Kunming, 650500, China.
- School of Ecology and Environmental Science, Yunnan University, Kunming, 650091, China.
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Guevara EE, Greene LK, Blanco MB, Farmer C, Ranaivonasy J, Ratsirarson J, Mahefarisoa KL, Rajaonarivelo T, Rakotondrainibe HH, Junge RE, Williams CV, Rambeloson E, Rasoanaivo HA, Rahalinarivo V, Andrianandrianina LH, Clayton JB, Rothman RS, Lawler RR, Bradley BJ, Yoder AD. Molecular Adaptation to Folivory and the Conservation Implications for Madagascar’s Lemurs. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.736741] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The lemurs of Madagascar include numerous species characterized by folivory across several families. Many extant lemuriform folivores exist in sympatry in Madagascar’s remaining forests. These species avoid feeding competition by adopting different dietary strategies within folivory, reflected in behavioral, morphological, and microbiota diversity across species. These conditions make lemurs an ideal study system for understanding adaptation to leaf-eating. Most folivorous lemurs are also highly endangered. The significance of folivory for conservation outlook is complex. Though generalist folivores may be relatively well equipped to survive habitat disturbance, specialist folivores occupying narrow dietary niches may be less resilient. Characterizing the genetic bases of adaptation to folivory across species and lineages can provide insights into their differential physiology and potential to resist habitat change. We recently reported accelerated genetic change in RNASE1, a gene encoding an enzyme (RNase 1) involved in molecular adaptation in mammalian folivores, including various monkeys and sifakas (genus Propithecus; family Indriidae). Here, we sought to assess whether other lemurs, including phylogenetically and ecologically diverse folivores, might show parallel adaptive change in RNASE1 that could underlie a capacity for efficient folivory. We characterized RNASE1 in 21 lemur species representing all five families and members of the three extant folivorous lineages: (1) bamboo lemurs (family Lemuridae), (2) sportive lemurs (family Lepilemuridae), and (3) indriids (family Indriidae). We found pervasive sequence change in RNASE1 across all indriids, a dN/dS value > 3 in this clade, and evidence for shared change in isoelectric point, indicating altered enzymatic function. Sportive and bamboo lemurs, in contrast, showed more modest sequence change. The greater change in indriids may reflect a shared strategy emphasizing complex gut morphology and microbiota to facilitate folivory. This case study illustrates how genetic analysis may reveal differences in functional traits that could influence species’ ecology and, in turn, their resilience to habitat change. Moreover, our results support the body of work demonstrating that not all primate folivores are built the same and reiterate the need to avoid generalizations about dietary guild in considering conservation outlook, particularly in lemurs where such diversity in folivory has probably led to extensive specialization via niche partitioning.
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Chen J, Huang X, Geng R, Zhu D, Wang W, Liu H. Ribonuclease1 contributes to the antibacterial response and immune defense in blunt snout bream (Megalobrama amblycephala). Int J Biol Macromol 2021; 172:309-320. [PMID: 33454323 DOI: 10.1016/j.ijbiomac.2021.01.066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/15/2020] [Accepted: 01/12/2021] [Indexed: 12/14/2022]
Abstract
Ribonuclease 1 (RNase1) is a vertebrate-specific enzyme that mainly performs digestive activity in herbivorous mammals. Here we used bacterial viability assays to explore its antimicrobial activity in blunt snout bream (Megalobrama amblycephala). The results showed that Ma-RNase1 rapidly killed Gram-negative and Gram-positive bacteria at micromolar concentrations. Ma-RNase1 increased the permeability of bacterial outer and inner membranes, thus reducing the integrity of bacterial cell wall and membrane. Moreover, Ma-RNase1 effectively counteracted the tissue damage and apoptosis caused by Aeromonas hydrophila infection. Quantitative real-time PCR and immunoblot analysis indicated that RNase1 mRNA and protein were up-regulated in the kidney and gut during infection. Furthermore, A. hydrophila infection significantly induced Tnf-α and Il-1β mRNA expression in liver, but not in the RNase1 pre-treatment group. In addition, a significant increase in the expression of immune-related genes (Nf-κb and Tlr4) was found in liver, kidney and gut of A. hydrophila-infected fish, while a decrease in Myd88 and Tlr4 levels was found in liver, spleen, kidney and gut in the group pre-treated with RNase1. Collectively, these data suggest that Ma-RNase1 has antimicrobial function both in vitro and in vivo, and contributes to the protective effect and immune defense of blunt snout bream.
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Affiliation(s)
- Jing Chen
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| | - Xin Huang
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| | - Ruijing Geng
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| | - Dongmei Zhu
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| | - Weimin Wang
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China.
| | - Han Liu
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China.
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Implication of Pseudo Reference Genes in Normalization of Data from Reverse Transcription-Quantitative PCR. Gene 2020; 757:144948. [DOI: 10.1016/j.gene.2020.144948] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 07/01/2020] [Accepted: 07/06/2020] [Indexed: 01/17/2023]
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Janiak MC, Burrell AS, Orkin JD, Disotell TR. Duplication and parallel evolution of the pancreatic ribonuclease gene (RNASE1) in folivorous non-colobine primates, the howler monkeys (Alouatta spp.). Sci Rep 2019; 9:20366. [PMID: 31889139 PMCID: PMC6937293 DOI: 10.1038/s41598-019-56941-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 12/13/2019] [Indexed: 12/27/2022] Open
Abstract
In foregut-fermenting mammals (e.g., colobine monkeys, artiodactyl ruminants) the enzymes pancreatic ribonuclease (RNASE1) and lysozyme C (LYZ), originally involved in immune defense, have evolved new digestive functions. Howler monkeys are folivorous non-colobine primates that lack the multi-chambered stomachs of colobines and instead digest leaves using fermentation in the caeco-colic region. We present data on the RNASE1 and LYZ genes of four species of howler monkey (Alouatta spp.). We find that howler monkey LYZ is conserved and does not share the substitutions found in colobine and cow sequences, whereas RNASE1 was duplicated in the common ancestor of A. palliata, A. seniculus, A. sara, and A. pigra. While the parent gene (RNASE1) is conserved, the daughter gene (RNASE1B) has multiple amino acid substitutions that are parallel to those found in RNASE1B genes of colobines. The duplicated RNase in Alouatta has biochemical changes similar to those in colobines, suggesting a novel, possibly digestive function. These findings suggest that pancreatic ribonuclease has, in parallel, evolved a new role for digesting the products of microbial fermentation in both foregut- and hindgut-fermenting folivorous primates. This may be a vital digestive enzyme adaptation allowing howler monkeys to survive on leaves during periods of low fruit availability.
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Affiliation(s)
- Mareike C Janiak
- Department of Anthropology, Rutgers University, New Brunswick, NJ, USA. .,Center for Human Evolutionary Studies, Rutgers University, New Brunswick, NJ, USA. .,Department of Anthropology & Archaeology, University of Calgary, Calgary, AB, Canada. .,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada.
| | - Andrew S Burrell
- Department of Anthropology, New York University, New York, NY, USA
| | - Joseph D Orkin
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Todd R Disotell
- Department of Anthropology, New York University, New York, NY, USA.,Department of Anthropology, University of Massachusetts, Amherst, MA, USA
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Lang D, Lim BK, Gao Y, Wang X. Adaptive evolutionary expansion of the ribonuclease 6 in Rodentia. Integr Zool 2019; 14:306-317. [PMID: 30688011 DOI: 10.1111/1749-4877.12382] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Ribonuclease 6 (RNase6 or RNase K6) is a protein that belongs to a superfamily thought to be the sole verte-brate-specific enzyme known for a wide range of physiological functions, including digestion, cytotoxicity, angiogenesis, male reproduction and host defense. In our study, 51 functional genes and 11 pseudogenes were identified from 27 Rodentia species. Intriguingly, in the 3 main lineages of rodents there were multiple RNase6s identified in all species of Ctenohystrica, whereas only a single RNase6 was observed in other Rodentia species examined except for 2 species in the mouse-related clade. The evolutionary scenario of "birth (gene duplication) and death (gene deactivation)" and gene sorting have been demonstrated in Ctenohystrica. In addition, bursts of positive selection, diversification of isoelectric point and positive net charge have been identified in Ctenohystrica, especially at two key sites that are involved in antimicrobial function. Site Trp30 has undergone positive selection and Ile45 has changed into other residues in Group B and Group C of the Ctenohystrica. Our results demonstrated a complex and intriguing evolutionary pattern of rodent RNase6, and indicated that functional modification may have occurred, which establishes an important theoretical foundation for future functional assays in rodent RNase6.
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Affiliation(s)
- Datian Lang
- Agronomy and Life Science Department, Zhaotong University, Zhaotong, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Science, Kunming, China
| | - Burton K Lim
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada
| | - Yun Gao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Science, Kunming, China
| | - Xiaoping Wang
- School of Life Sciences, Yunnan University, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan, Yunnan University, Kunming, China.,Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, Yunnan University, Kunming, China
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