1
|
Fu Y, Liang F, Li C, Warren A, Shin MK, Li L. Codon Usage Bias Analysis in Macronuclear Genomes of Ciliated Protozoa. Microorganisms 2023; 11:1833. [PMID: 37513005 PMCID: PMC10384029 DOI: 10.3390/microorganisms11071833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/12/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Ciliated protozoa (ciliates) are unicellular eukaryotes, several of which are important model organisms for molecular biology research. Analyses of codon usage bias (CUB) of the macronuclear (MAC) genome of ciliates can promote a better understanding of the genetic mode and evolutionary history of these organisms and help optimize codons to improve gene editing efficiency in model ciliates. In this study, the following indices were calculated: the guanine-cytosine (GC) content, the frequency of the nucleotides at the third position of codons (T3, C3, A3, G3), the effective number of codons (ENc), GC content at the 3rd position of synonymous codons (GC3s), and the relative synonymous codon usage (RSCU). Parity rule 2 plot analysis, Neutrality plot analysis, ENc plot analysis, and correlation analysis were employed to explore the main influencing factors of CUB. The results showed that the GC content in the MAC genomes of each of 21 ciliate species, the genomes of which were relatively complete, was lower than 50%, and the base compositions of GC and GC3s were markedly distinct. Synonymous codon analysis revealed that the codons in most of the 21 ciliates ended with A or T and four codons were the general putative optimal codons. Collectively, our results indicated that most of the ciliates investigated preferred using the codons with anof AT-ending and that codon usage bias was affected by gene mutation and natural selection.
Collapse
Affiliation(s)
- Yu Fu
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China
| | - Fasheng Liang
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China
| | - Congjun Li
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
| | - Mann Kyoon Shin
- Department of Biology, University of Ulsan, Ulsan 44610, Republic of Korea
| | - Lifang Li
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China
| |
Collapse
|
2
|
Park T, Wijeratne S, Meulia T, Firkins JL, Yu Z. The macronuclear genome of anaerobic ciliate Entodinium caudatum reveals its biological features adapted to the distinct rumen environment. Genomics 2021; 113:1416-1427. [PMID: 33722656 DOI: 10.1016/j.ygeno.2021.03.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 02/02/2021] [Accepted: 03/05/2021] [Indexed: 10/21/2022]
Abstract
Entodinium caudatum is an anaerobic binucleated ciliate representing the most dominant protozoal species in the rumen. However, its biological features are largely unknown due to the inability to establish an axenic culture. In this study, we primally sequenced its macronucleus (MAC) genome to aid the understanding of its metabolism, physiology, ecology. We isolated the MAC of E. caudatum strain MZG-1 and sequenced the MAC genome using Illumina MiSeq, MinION, and PacBio RSII systems. De novo assembly of the MiSeq sequence reads followed with subsequent scaffolding with MinION and PacBio reads resulted in a draft MAC genome about 117 Mbp. A large number of carbohydrate-active enzymes were likely acquired through horizontal gene transfer. About 8.74% of the E. caudatum predicted proteome was predicted as proteases. The MAC genome of E. caudatum will help better understand its important roles in rumen carbohydrate metabolism, and interaction with other members of the rumen microbiome.
Collapse
Affiliation(s)
- Tansol Park
- Department of Animal Sciences, The Ohio State University, Columbus, OH, 43210, USA
| | - Saranga Wijeratne
- Molecular and Cellular Imaging Center, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, 44691, USA
| | - Tea Meulia
- Molecular and Cellular Imaging Center, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, 44691, USA; Department of Plant Pathology, The Ohio State University, Wooster, OH, 44691, USA
| | - Jeffrey L Firkins
- Department of Animal Sciences, The Ohio State University, Columbus, OH, 43210, USA
| | - Zhongtang Yu
- Department of Animal Sciences, The Ohio State University, Columbus, OH, 43210, USA.
| |
Collapse
|
3
|
Williams CL, Thomas BJ, McEwan NR, Rees Stevens P, Creevey CJ, Huws SA. Rumen Protozoa Play a Significant Role in Fungal Predation and Plant Carbohydrate Breakdown. Front Microbiol 2020; 11:720. [PMID: 32411103 PMCID: PMC7200989 DOI: 10.3389/fmicb.2020.00720] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 03/27/2020] [Indexed: 11/23/2022] Open
Abstract
The rumen protozoa, alongside fungi, comprise the eukaryotic portion of the rumen microbiome. Rumen protozoa may account for up to 50% of biomass, yet their role in this ecosystem remains unclear. Early experiments inferred a role in carbohydrate and protein metabolism, but due to their close association with bacteria, definitively attributing these functions to the protozoa was challenging. The advent of ‘omic technologies has created opportunities to broaden our understanding of the rumen protozoa. This study aimed to utilize these methods to further our understanding of the role that protozoa play in the rumen in terms of their metabolic capacities, and in doing so, contribute valuable sequence data to reduce the chance of mis or under-representation of the rumen protozoa in meta’omic datasets. Rumen protozoa were isolated and purified using glucose-based sedimentation and differential centrifugation, extracted RNA was Poly(A) fraction enriched and DNase treated before use in a phage-based, cDNA metatranscriptomic library. Biochemical activity testing of the phage library showed 6 putatively positive plaques in response to carboxymethyl cellulose agar (indicative of cellulose activity), and no positive results for tributyrin (indicative of esterase/lipase activity) or egg yolk agar (indicative of proteolysis). Direct sequencing of the cDNA was also conducted using the Illumina HiSeq 2500. The metatranscriptome identified a wealth of carbohydrate-active enzymes which accounted for 8% of total reads. The most highly expressed carbohydrate-active enzymes were glycosyl hydrolases 5 and 11, polysaccharide lyases and deacetylases, xylanases and enzymes active against pectin, mannan and chitin; the latter likely used to digest rumen fungi which contain a chitin-rich cell membrane. Codon usage analysis of expressed genes also showed evidence of horizontal gene transfer, suggesting that many of these enzymes were acquired from the rumen bacteria in an evolutionary response to the carbohydrate-rich environment of the rumen. This study provides evidence of the significant contribution that the protozoa make to carbohydrate breakdown in the rumen, potentially using horizontally acquired genes, and highlights their predatory capacity.
Collapse
Affiliation(s)
- Cate L Williams
- Institute of Biological, Environmental and Rural Science, Aberystwyth University, Aberystwyth, United Kingdom
| | - Benjamin J Thomas
- School of Biological Sciences, Institute for Global Food Security, Queen's University Belfast, Belfast, United Kingdom
| | - Neil R McEwan
- School of Pharmacy and Life Sciences, Robert Gordon University, Aberdeen, United Kingdom
| | - Pauline Rees Stevens
- Institute of Biological, Environmental and Rural Science, Aberystwyth University, Aberystwyth, United Kingdom
| | - Christopher J Creevey
- School of Biological Sciences, Institute for Global Food Security, Queen's University Belfast, Belfast, United Kingdom
| | - Sharon A Huws
- School of Biological Sciences, Institute for Global Food Security, Queen's University Belfast, Belfast, United Kingdom
| |
Collapse
|
4
|
Feng JM, Jiang CQ, Sun ZY, Hua CJ, Wen JF, Miao W, Xiong J. Single-cell transcriptome sequencing of rumen ciliates provides insight into their molecular adaptations to the anaerobic and carbohydrate-rich rumen microenvironment. Mol Phylogenet Evol 2019; 143:106687. [PMID: 31740334 DOI: 10.1016/j.ympev.2019.106687] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 11/11/2019] [Accepted: 11/13/2019] [Indexed: 01/26/2023]
Abstract
Rumen ciliates are a specialized group of ciliates exclusively found in the anaerobic, carbohydrate-rich rumen microenvironment. However, the molecular and mechanistic basis of the physiological and behavioral adaptation of ciliates to the rumen microenvironment is undefined. We used single-cell transcriptome sequencing to explore the adaptive evolution of three rumen ciliates: two entodiniomorphids, Entodinium furca and Diplodinium dentatum; and one vestibuliferid, Isotricha intestinalis. We found that all three species are members of monophyletic orders within the class Litostomatea, with E. furca and D. dentatum in Entodiniomorphida and I. intestinalis in Vestibuliferida. The two entodiniomorphids might use H2-producing mitochondria and the vestibuliferid might use anaerobic mitochondria to survive under strictly anaerobic conditions. Moreover, carbohydrate-active enzyme (CAZyme) genes were identified in all three species, including cellulases, hemicellulases, and pectinases. The evidence that all three species have acquired prokaryote-derived genes by horizontal gene transfer (HGT) to digest plant biomass includes a significant enrichment of gene ontology categories such as cell wall macromolecule catabolic process and carbohydrate catabolic process and the identification of genes in common between CAZyme and HGT groups. These findings suggest that HGT might be an important mechanism in the adaptive evolution of ciliates to the rumen microenvironment.
Collapse
Affiliation(s)
- Jin-Mei Feng
- Department of Pathogenic Biology, School of Medicine, Jianghan University, Wuhan 430056, China
| | - Chuan-Qi Jiang
- Shenzhen Institute of Guangdong Ocean University, Shenzhen 518120, China; Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen 518120, China; Shenzhen Dapeng New District Science and Technology Innovation Service Center, Shenzhen 518119, China; Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Zong-Yi Sun
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Cong-Jie Hua
- Department of Pathogenic Biology, School of Medicine, Jianghan University, Wuhan 430056, China
| | - Jian-Fan Wen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Wei Miao
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; State Key Laboratory of Freshwater Ecology and Biotechnology of China, Wuhan 430072, China; CAS Center for Excellence in Animal Evolution and Genetics, Kunming 650223, China.
| | - Jie Xiong
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
| |
Collapse
|
5
|
Characterisation of the effect of day length, and associated differences in dietary intake, on the gut microbiota of Soay sheep. Arch Microbiol 2019; 201:889-896. [PMID: 30968220 PMCID: PMC6687699 DOI: 10.1007/s00203-019-01652-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 03/08/2019] [Accepted: 03/13/2019] [Indexed: 11/24/2022]
Abstract
Differences in the rumen bacterial community have been previously reported for Soay sheep housed under different day length conditions. This study extends this previous investigation to other organs of the digestive tract, as well as the analysis of ciliated protozoa and anaerobic fungi. The detectable concentrations of ciliated protozoa and anaerobic fungi decreased with increased day length in both the rumen and large colon, unlike those of bacteria where no effect was observed. Conversely, bacterial community composition was affected by day length in both the rumen and large colon, but the community composition of the detectable ciliated protozoa and anaerobic fungi was not affected. Day length-associated differences in the bacterial community composition extended to all of the organs examined, with the exception of the duodenum and the jejunum. It is proposed that differences in rumen fill and ruminal ‘by-pass’ nutrients together with endocrinological changes cause the observed effects of day length on the different gut microbial communities.
Collapse
|
6
|
Newbold CJ, de la Fuente G, Belanche A, Ramos-Morales E, McEwan NR. The Role of Ciliate Protozoa in the Rumen. Front Microbiol 2015; 6:1313. [PMID: 26635774 PMCID: PMC4659874 DOI: 10.3389/fmicb.2015.01313] [Citation(s) in RCA: 301] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 11/09/2015] [Indexed: 01/17/2023] Open
Abstract
First described in 1843, Rumen protozoa with their striking appearance were assumed to be important for the welfare of their host. However, despite contributing up to 50% of the bio-mass in the rumen, the role of protozoa in rumen microbial ecosystem remains unclear. Phylogenetic analysis of 18S rDNA libraries generated from the rumen of cattle, sheep, and goats has revealed an unexpected diversity of ciliated protozoa although variation in gene copy number between species makes it difficult to obtain absolute quantification. Despite repeated attempts it has proven impossible to maintain rumen protozoa in axenic culture. Thus it has been difficult to establish conclusively a role of ciliate protozoa in rumen fiber degradation. The development of techniques to clone and express ciliate genes in λ phage, together with bioinformatic indices to confirm the ciliate origin of the genes has allowed the isolation and characterization of fibrolytic genes from rumen protozoa. Elimination of the ciliate protozoa increases microbial protein supply by up to 30% and reduces methane production by up to 11%. Our recent findings suggest that holotrich protozoa play a disproportionate role in supporting methanogenesis whilst the small Entodinium are responsible for much of the bacterial protein turnover. As yet no method to control protozoa in the rumen that is safe and practically applicable has been developed, however a range of plant extract capable of controlling if not completely eliminating rumen protozoa have been described.
Collapse
Affiliation(s)
- Charles J. Newbold
- Institute of Biological Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Gabriel de la Fuente
- Departament de Producció Animal, Escola Tècnica Superior d’Enginyeria Agrària, Universitat de Lleida, Lleida, Spain
| | - Alejandro Belanche
- Institute of Biological Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Eva Ramos-Morales
- Institute of Biological Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Neil R. McEwan
- Institute of Biological Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| |
Collapse
|
7
|
Activity-based metagenomic screening and biochemical characterization of bovine ruminal protozoan glycoside hydrolases. Appl Environ Microbiol 2011; 77:8106-13. [PMID: 21948825 DOI: 10.1128/aem.05925-11] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The rumen, the foregut of herbivorous ruminant animals such as cattle, functions as a bioreactor to process complex plant material. Among the numerous and diverse microbes involved in ruminal digestion are the ruminal protozoans, which are single-celled, ciliated eukaryotic organisms. An activity-based screen was executed to identify genes encoding fibrolytic enzymes present in the metatranscriptome of a bovine ruminal protozoan-enriched cDNA expression library. Of the four novel genes identified, two were characterized in biochemical assays. Our results provide evidence for the effective use of functional metagenomics to retrieve novel enzymes from microbial populations that cannot be maintained in axenic cultures.
Collapse
|
8
|
Shi PJ, Meng K, Zhou ZG, Wang YR, Diao QY, Yao B. The host species affects the microbial community in the goat rumen. Lett Appl Microbiol 2007; 46:132-5. [PMID: 17971095 DOI: 10.1111/j.1472-765x.2007.02274.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS This study was carried out to determine whether bacterial and ciliate populations in goat rumen vary significantly between different goat species living in the same environment. METHODS AND RESULTS Bacterial and ciliate communities in the rumen of three goat species were analysed at the molecular level using denaturing gradient gel electrophoresis. The microbial community varied considerably among goats living in the same environment. Interspecies variation in the bacterial population was noticeably greater than intraspecies variation. In contrast, there was considerable variation in the ciliate population among goats within the same species, and intraspecies similarities were no greater than those observed across species. CONCLUSIONS Because environmental factors and diets were identical for all goats, differences in bacterial populations reflect species-specific differences in rumen microbes. SIGNIFICANCE AND IMPACT OF THE STUDY Factors related to the host species have an important effect on determining the bacterial composition in the goat rumen.
Collapse
Affiliation(s)
- P J Shi
- Microbial Engineering Department, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | | | | | | | | | | |
Collapse
|
9
|
Ricard G, McEwan NR, Dutilh BE, Jouany JP, Macheboeuf D, Mitsumori M, McIntosh FM, Michalowski T, Nagamine T, Nelson N, Newbold CJ, Nsabimana E, Takenaka A, Thomas NA, Ushida K, Hackstein JHP, Huynen MA. Horizontal gene transfer from Bacteria to rumen Ciliates indicates adaptation to their anaerobic, carbohydrates-rich environment. BMC Genomics 2006; 7:22. [PMID: 16472398 PMCID: PMC1413528 DOI: 10.1186/1471-2164-7-22] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2005] [Accepted: 02/10/2006] [Indexed: 12/04/2022] Open
Abstract
Background The horizontal transfer of expressed genes from Bacteria into Ciliates which live in close contact with each other in the rumen (the foregut of ruminants) was studied using ciliate Expressed Sequence Tags (ESTs). More than 4000 ESTs were sequenced from representatives of the two major groups of rumen Cilates: the order Entodiniomorphida (Entodinium simplex, Entodinium caudatum, Eudiplodinium maggii, Metadinium medium, Diploplastron affine, Polyplastron multivesiculatum and Epidinium ecaudatum) and the order Vestibuliferida, previously called Holotricha (Isotricha prostoma, Isotricha intestinalis and Dasytricha ruminantium). Results A comparison of the sequences with the completely sequenced genomes of Eukaryotes and Prokaryotes, followed by large-scale construction and analysis of phylogenies, identified 148 ciliate genes that specifically cluster with genes from the Bacteria and Archaea. The phylogenetic clustering with bacterial genes, coupled with the absence of close relatives of these genes in the Ciliate Tetrahymena thermophila, indicates that they have been acquired via Horizontal Gene Transfer (HGT) after the colonization of the gut by the rumen Ciliates. Conclusion Among the HGT candidates, we found an over-representation (>75%) of genes involved in metabolism, specifically in the catabolism of complex carbohydrates, a rich food source in the rumen. We propose that the acquisition of these genes has greatly facilitated the Ciliates' colonization of the rumen providing evidence for the role of HGT in the adaptation to new niches.
Collapse
Affiliation(s)
- Guénola Ricard
- Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands
| | - Neil R McEwan
- Institute of Rural Sciences, University of Wales, Aberystwyth, SY23 3AL, UK
| | - Bas E Dutilh
- Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands
| | - Jean-Pierre Jouany
- I.N.R.A., Station de Recherches sur la Nutrition des Herbivores, Centre de Recherches de Clermont-Ferrand/Theix, France
| | - Didier Macheboeuf
- I.N.R.A., Station de Recherches sur la Nutrition des Herbivores, Centre de Recherches de Clermont-Ferrand/Theix, France
| | - Makoto Mitsumori
- National Institute of Livestock and Grassland Science, 2 Ikenodai, Kukizaki, Ibaraki, 305-0901, Japan
| | | | - Tadeusz Michalowski
- Kielanowski Institute of Animal Physiology and Nutrition, Polish Academy of Sciences, Jablonna, Warsaw, Poland
| | - Takafumi Nagamine
- Rumen Microbiology Research Team, STAFF-Institute, 446-1 Ippaizuka, Kamiyokoba, Tsukuba 305-0854, Japan
| | - Nancy Nelson
- Rowett Research Institute, Aberdeen, AB21 9SB, UK
| | - Charles J Newbold
- Rumen Microbiology Research Team, STAFF-Institute, 446-1 Ippaizuka, Kamiyokoba, Tsukuba 305-0854, Japan
| | - Eli Nsabimana
- I.N.R.A., Station de Recherches sur la Nutrition des Herbivores, Centre de Recherches de Clermont-Ferrand/Theix, France
| | - Akio Takenaka
- National Institute of Livestock and Grassland Science, 2 Ikenodai, Kukizaki, Ibaraki, 305-0901, Japan
| | | | - Kazunari Ushida
- Laboratory of Animal Science, Kyoto Prefectural University, Shimogamo, Kyoto 606-8522, Japan
| | - Johannes HP Hackstein
- Department of Evolutionary Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Martijn A Huynen
- Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands
| |
Collapse
|
10
|
Newbold CJ, McEwan NR, Calza RE, Chareyron EN, Duval SM, Eschenlauer SCP, McIntosh FM, Nelson N, Travis AJ, Wallace RJ. An NAD+-dependent glutamate dehydrogenase cloned from the ruminal ciliate protozoan,Entodinium caudatum. FEMS Microbiol Lett 2005; 247:113-21. [PMID: 15921862 DOI: 10.1016/j.femsle.2005.04.034] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2005] [Revised: 04/21/2005] [Accepted: 04/23/2005] [Indexed: 11/28/2022] Open
Abstract
An NAD(+)-dependent glutamate dehydrogenase (GDH; EC 1.4.1.24) was cloned from the ruminal ciliate protozoan, Entodinium caudatum. The gene had high sequence similarity to GDH genes from the Bacteroides (class)--a class of bacteria which is highly represented in the rumen. When expressed in Escherichia coli the enzyme had a high affinity for ammonia and alpha-ketoglutarate (apparent K(m) of 2.33 and 0.71 mM, respectively) and a low affinity for glutamate (apparent K(m) of 98 mM). GDH activity and GDH mRNA concentration were increased by incubating washed E. caudatum cells with ammonia and antibiotics. These results suggest that the GDH is an anabolic enzyme catalysing the assimilation of ammonia by E. caudatum in the rumen and that the gene was probably acquired by lateral gene transfer from a ruminal bacterium.
Collapse
Affiliation(s)
- C James Newbold
- Rowett Research Institute, Greenburn Road, Aberdeen AB21 9SB, Scotland, United Kingdom
| | | | | | | | | | | | | | | | | | | |
Collapse
|
11
|
Béra-Maillet C, Devillard E, Cezette M, Jouany JP, Forano E. Xylanases and carboxymethylcellulases of the rumen protozoaPolyplastron multivesiculatum,Eudiplodinium maggiiandEntodiniumsp. FEMS Microbiol Lett 2005; 244:149-56. [PMID: 15727834 DOI: 10.1016/j.femsle.2005.01.035] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2004] [Revised: 10/27/2004] [Accepted: 01/20/2005] [Indexed: 11/20/2022] Open
Abstract
Endoglucanase and xylanase activities of three rumen protozoa, Polyplastron multivesiculatum, Eudiplodinium maggii, and Entodinium sp. were compared qualitatively by zymograms and quantitatively by measuring specific activities against different polysaccharides. A set of carboxymethylcellulases and xylanases was produced by the large ciliates whereas no band of activity was observed for Entodinium sp. in zymograms. Specific activity of endoglucanases from P. multivesiculatum (1.3 micromol mg prot(-1) min(-1)) was twice that of E. maggii, whereas xylanase specific activity (4.5 micromol mg prot(-1) min(-1)) was only half. Very weak activities were observed for Entodinium sp. A new xylanase gene, xyn11D, from P. multivesiculatum was reported and its gene product compared to 33 other family 11 xylanases. Phylogenetic analysis showed that xylanase sequences from rumen protozoa are closely related to those of bacteria.
Collapse
Affiliation(s)
- Christel Béra-Maillet
- Unité de Microbiologie, INRA, Centre de Recherches de Clermont-Ferrand-Theix, 63122 Saint-Genès-Champanelle, France.
| | | | | | | | | |
Collapse
|
12
|
Devillard E, Bera-Maillet C, Flint HJ, Scott KP, Newbold CJ, Wallace RJ, Jouany JP, Forano E. Characterization of XYN10B, a modular xylanase from the ruminal protozoan Polyplastron multivesiculatum, with a family 22 carbohydrate-binding module that binds to cellulose. Biochem J 2003; 373:495-503. [PMID: 12693992 PMCID: PMC1223500 DOI: 10.1042/bj20021784] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2002] [Revised: 04/04/2003] [Accepted: 04/14/2003] [Indexed: 11/17/2022]
Abstract
A new xylanase gene, xyn10B, was isolated from the ruminal protozoan Polyplastron multivesiculatum and the gene product was characterized. XYN10B is the first protozoan family 10 glycoside hydrolase characterized so far and is a modular enzyme comprising a family 22 carbohydrate-binding module (CBM) preceding the catalytic domain. The CBM22 was shown to be a true CBM. It showed high affinity for soluble arabinoxylan and is the first example of a CBM22 that binds strongly to celluloses of various crystallinities. The enzymic properties of XYN10B were also analysed. Its optimal temperature and pH for activity were 39 degrees C and 7.0 respectively; these values being close to those of the ruminal ecosystem. The phylogenetic relationships between the XYN10B CBM22 or catalytic domain and related sequences from ruminal and non-ruminal bacteria and eukaryotes are reported. The xyn10B gene is shown to lack introns.
Collapse
Affiliation(s)
- Estelle Devillard
- Rowett Research Institute, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, UK
| | | | | | | | | | | | | | | |
Collapse
|
13
|
McEwan NR, Eschenlauer SC, Calza RE, Wallace RJ, Newbold CJ. The 3' untranslated region of messages in the rumen protozoan Entodinium caudatum. Protist 2000; 151:139-46. [PMID: 10965953 DOI: 10.1078/1434-4610-00014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The 3' untranslated regions of a number of cDNAs from the rumen protozoal species Entodinium caudatum were studied with a view to characterising their preference for stop codons, general length, nucleotide composition and polyadenylation signals. Unlike a number of ciliates, Entodinium caudatum uses UAA as a stop codon, rather than as a codon for glutamine. In addition, the 3' untranslated region of the message is generally less than 100 nucleotides in length, extremely A+T rich, and does not appear to utilise any of the conventional polyadenylation signals described in other organisms.
Collapse
Affiliation(s)
- N R McEwan
- Rowett Research Institute, Bucksburn, Aberdeen, Scotland.
| | | | | | | | | |
Collapse
|
14
|
McEwan NR, Gatherer D, Eschenlauer SC, McIntosh FM, Calza RE, John Wallace R, Jamie Newbold C. An Unusual Codon Usage Pattern in the Ciliate Family Ophryoscolecidae and its Implications for Determining the Source of Cloned DNA. Anaerobe 2000. [DOI: 10.1006/anae.1999.0310] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
15
|
Devillard E, Newbold CJ, Scott KP, Forano E, Wallace RJ, Jouany JP, Flint HJ. A xylanase produced by the rumen anaerobic protozoan Polyplastron multivesiculatum shows close sequence similarity to family 11 xylanases from gram-positive bacteria. FEMS Microbiol Lett 1999; 181:145-52. [PMID: 10564800 DOI: 10.1111/j.1574-6968.1999.tb08837.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
We report for the first time the cloning and characterisation of a protozoal enzyme involved in plant cell wall polysaccharide degradation. A cDNA library was constructed from the ruminal protozoan Polyplastron multivesiculatum and a stable clone expressing xylanase activity was isolated. The encoded enzyme belongs to the glycoside hydrolase family 11, and phylogenetic analysis indicates a closer relationship with catalytic domains from Gram-positive bacteria than the other fibrolytic eukaryotes from the rumen, the anaerobic fungi.
Collapse
Affiliation(s)
- E Devillard
- Rowett Research Institute, Bucksburn, Aberdeen, UK
| | | | | | | | | | | | | |
Collapse
|