1
|
Jeena NS, Rahuman S, Sebastian W, Kumar R, Sajeela KA, Kizhakudan JK, Menon KK, Roul SK, Gopalakrishnan A, Radhakrishnan EV. Mitogenomic recognition of incognito lineages in the mud spiny lobster Panulirus polyphagus (Herbst, 1793): A tale of unique genetic structuring and diversification. Int J Biol Macromol 2024; 277:134327. [PMID: 39098694 DOI: 10.1016/j.ijbiomac.2024.134327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 07/23/2024] [Accepted: 07/25/2024] [Indexed: 08/06/2024]
Abstract
This study provides the first documentation of three deep conspecific lineages within Panulirus polyphagus in the Indian Ocean, bridging the gap in genetic research. Comparative mitogenomics between lineages (L) at both species and family levels, evolutionary relationships and heterogeneity of sequence divergence within Decapoda, and divergence time estimation were performed. The characterized mitogenomes ranged from 15,685-15,705 bp in size and exhibited a typical pancrustacean pattern. Among the three lineages, L1 predominated the Bay of Bengal, L2 the Arabian Sea, and L2.a, a less common lineage genetically closer to L2, was restricted to the latter region. A minor lineage L1.a, was observed in the Coral Triangle area. All PCGs displayed evidence of purifying selection across species and family levels. The largest genetic distance (K2P) between lineages was 9 %, notably between L1.a and L2.a. The phylogenetic tree subdivided the Achelates into Palinuridae and Scyllaridae, and the topology demonstrated a distinct pattern of lineage diversification within P. polyphagus. AliGROOVE analysis revealed no discernible divergence in Decapoda. The diversification of P. polyphagus appears to have occurred during Miocene, with further diversification in Pliocene. Furthermore, genetic stocks and population connectivity recognized here will provide valuable insight for spatial management planning of this dwindling resource.
Collapse
Affiliation(s)
- N S Jeena
- Marine Biotechnology, Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Kochi, Kerala, India.
| | - Summaya Rahuman
- Marine Biotechnology, Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Kochi, Kerala, India
| | - Wilson Sebastian
- Centre for Marine Living Resources and Ecology (CMLRE), Kochi, Kerala, India
| | - Rajan Kumar
- Shellfish Fisheries Division, Regional Station of CMFRI, Veraval, Gujarat, India
| | - K A Sajeela
- Marine Biotechnology, Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Kochi, Kerala, India
| | - Joe K Kizhakudan
- Mariculture Division, Regional Centre of CMFRI, Visakhapatnam, Andhra Pradesh, India
| | | | - Subal Kumar Roul
- Finfish Fisheries Division, Regional Station of CMFRI, Digha, West Bengal, India
| | | | | |
Collapse
|
2
|
Wang Z, Zhang S, Geng Z, Li C, Sun L, Zhang L, Cao Z. Soil bacterial community diversity and life strategy during slope restoration on an uninhabited island: changes under the aggregate spray-seeding technique. J Appl Microbiol 2024; 135:lxae132. [PMID: 38830801 DOI: 10.1093/jambio/lxae132] [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: 02/07/2024] [Revised: 05/29/2024] [Accepted: 05/31/2024] [Indexed: 06/05/2024]
Abstract
AIMS We investigated the effects of the aggregate spray-seeding (ASS) technique on soil bacterial community diversity, life strategies, and seasonal change. METHODS AND RESULTS Soil from six plots with original vegetation (CK, n = 6) was compared to soil from 15 plots with spray-seeding restoration (SR, n = 15) using environmental DNA sequencing. The bacterial Shannon and Chao1 indices of SR soils were significantly greater (P < 0.05) than those of CK soils. The Chao1 index for the SR soil bacterial community was significantly greater in summer (P < 0.05) than in winter. The ratio of the relative abundance of bacterial K-strategists to r-strategists (K/r) and the DNA guanine-cytosine (GC) content in the SR soil were significantly lower (P < 0.05) than those in the CK soil. Principal coordinate analysis revealed significant differences between the SR and CK bacterial communities. The GC content was positively correlated with the K/r ratio. Soil conductivity was negatively associated with the K/r ratio and GC content, indicating that ionic nutrients were closely related to bacterial life strategies. CONCLUSIONS The ASS technique improved soil bacterial diversity, altered community composition, and favored bacterial r-strategists.
Collapse
Affiliation(s)
- Zhikang Wang
- Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture; College of Natural Resources and Environment, Northwest A & F University, Yangling 712100, China
- Qingdao Greensum Ecology Co., Ltd., Qingdao 266102, China
| | - Shilei Zhang
- Qingdao Greensum Ecology Co., Ltd., Qingdao 266102, China
| | - Zengchao Geng
- Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture; College of Natural Resources and Environment, Northwest A & F University, Yangling 712100, China
| | - Chunlin Li
- Qingdao Greensum Ecology Co., Ltd., Qingdao 266102, China
| | - Linting Sun
- Qingdao Greensum Ecology Co., Ltd., Qingdao 266102, China
| | | | - Zhiquan Cao
- Qingdao Greensum Ecology Co., Ltd., Qingdao 266102, China
| |
Collapse
|
3
|
Kapoor S, Yang YT, Hall RN, Gasser RB, Bowles VM, Perry T, Anstead CA. Complete Mitochondrial Genome for Lucilia cuprina dorsalis (Diptera: Calliphoridae) from the Northern Territory, Australia. Genes (Basel) 2024; 15:506. [PMID: 38674440 PMCID: PMC11050061 DOI: 10.3390/genes15040506] [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: 03/20/2024] [Revised: 04/09/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
The Australian sheep blowfly, Lucilia cuprina dorsalis, is a major sheep ectoparasite causing subcutaneous myiasis (flystrike), which can lead to reduced livestock productivity and, in severe instances, death of the affected animals. It is also a primary colonizer of carrion, an efficient pollinator, and used in maggot debridement therapy and forensic investigations. In this study, we report the complete mitochondrial (mt) genome of L. c. dorsalis from the Northern Territory (NT), Australia, where sheep are prohibited animals, unlike the rest of Australia. The mt genome is 15,943 bp in length, comprising 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs), and a non-coding control region. The gene order of the current mt genome is consistent with the previously published L. cuprina mt genomes. Nucleotide composition revealed an AT bias, accounting for 77.5% of total mt genome nucleotides. Phylogenetic analyses of 56 species/taxa of dipterans indicated that L. c. dorsalis and L. sericata are the closest among all sibling species of the genus Lucilia, which helps to explain species evolution within the family Luciliinae. This study provides the first complete mt genome sequence for L. c. dorsalis derived from the NT, Australia to facilitate species identification and the examination of the evolutionary history of these blowflies.
Collapse
Affiliation(s)
- Shilpa Kapoor
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia; (Y.T.Y.); (T.P.)
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia; (R.B.G.); (V.M.B.)
| | - Ying Ting Yang
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia; (Y.T.Y.); (T.P.)
| | - Robyn N. Hall
- CSIRO Health & Biosecurity, Acton, ACT 2601, Australia;
- Ausvet Pty Ltd., Fremantle, WA 6160, Australia
| | - Robin B. Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia; (R.B.G.); (V.M.B.)
| | - Vernon M. Bowles
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia; (R.B.G.); (V.M.B.)
| | - Trent Perry
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia; (Y.T.Y.); (T.P.)
| | - Clare A. Anstead
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia; (R.B.G.); (V.M.B.)
| |
Collapse
|
4
|
Wu Y, Gao N, Sun C, Feng T, Liu Q, Chen WH. A compendium of ruminant gastrointestinal phage genomes revealed a higher proportion of lytic phages than in any other environments. MICROBIOME 2024; 12:69. [PMID: 38576042 PMCID: PMC10993611 DOI: 10.1186/s40168-024-01784-2] [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: 03/20/2023] [Accepted: 02/29/2024] [Indexed: 04/06/2024]
Abstract
BACKGROUND Ruminants are important livestock animals that have a unique digestive system comprising multiple stomach compartments. Despite significant progress in the study of microbiome in the gastrointestinal tract (GIT) sites of ruminants, we still lack an understanding of the viral community of ruminants. Here, we surveyed its viral ecology using 2333 samples from 10 sites along the GIT of 8 ruminant species. RESULTS We present the Unified Ruminant Phage Catalogue (URPC), a comprehensive survey of phages in the GITs of ruminants including 64,922 non-redundant phage genomes. We characterized the distributions of the phage genomes in different ruminants and GIT sites and found that most phages were organism-specific. We revealed that ~ 60% of the ruminant phages were lytic, which was the highest as compared with those in all other environments and certainly will facilitate their applications in microbial interventions. To further facilitate the future applications of the phages, we also constructed a comprehensive virus-bacteria/archaea interaction network and identified dozens of phages that may have lytic effects on methanogenic archaea. CONCLUSIONS The URPC dataset represents a useful resource for future microbial interventions to improve ruminant production and ecological environmental qualities. Phages have great potential for controlling pathogenic bacterial/archaeal species and reducing methane emissions. Our findings provide insights into the virome ecology research of the ruminant GIT and offer a starting point for future research on phage therapy in ruminants. Video Abstract.
Collapse
Affiliation(s)
- Yingjian Wu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Center for Artificial Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Na Gao
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Chuqing Sun
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Center for Artificial Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Tong Feng
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Center for Artificial Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Qingyou Liu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China.
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China.
| | - Wei-Hua Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Center for Artificial Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China.
- Institution of Medical Artificial Intelligence, Binzhou Medical University, Yantai, 264003, China.
| |
Collapse
|
5
|
Kaplan NA, Islam KN, Kanis FC, Verderber JR, Wang X, Jones JA, Koffas MAG. Simultaneous glucose and xylose utilization by an Escherichia coli catabolite repression mutant. Appl Environ Microbiol 2024; 90:e0216923. [PMID: 38289128 PMCID: PMC10880614 DOI: 10.1128/aem.02169-23] [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: 12/01/2023] [Accepted: 12/11/2023] [Indexed: 02/22/2024] Open
Abstract
As advances are made toward the industrial feasibility of mass-producing biofuels and commodity chemicals with sugar-fermenting microbes, high feedstock costs continue to inhibit commercial application. Hydrolyzed lignocellulosic biomass represents an ideal feedstock for these purposes as it is cheap and prevalent. However, many microbes, including Escherichia coli, struggle to efficiently utilize this mixture of hexose and pentose sugars due to the regulation of the carbon catabolite repression (CCR) system. CCR causes a sequential utilization of sugars, rather than simultaneous utilization, resulting in reduced carbon yield and complex process implications in fed-batch fermentation. A mutant of the gene encoding the cyclic AMP receptor protein, crp*, has been shown to disable CCR and improve the co-utilization of mixed sugar substrates. Here, we present the strain construction and characterization of a site-specific crp* chromosomal mutant in E. coli BL21 star (DE3). The crp* mutant strain demonstrates simultaneous consumption of glucose and xylose, suggesting a deregulated CCR system. The proteomics further showed that glucose was routed to the C5 carbon utilization pathways to support both de novo nucleotide synthesis and energy production in the crp* mutant strain. Metabolite analyses further show that overflow metabolism contributes to the slower growth in the crp* mutant. This highly characterized strain can be particularly beneficial for chemical production by simultaneously utilizing both C5 and C6 substrates from lignocellulosic biomass.IMPORTANCEAs the need for renewable biofuel and biochemical production processes continues to grow, there is an associated need for microbial technology capable of utilizing cheap, widely available, and renewable carbon substrates. This work details the construction and characterization of the first B-lineage Escherichia coli strain with mutated cyclic AMP receptor protein, Crp*, which deregulates the carbon catabolite repression (CCR) system and enables the co-utilization of multiple sugar sources in the growth medium. In this study, we focus our analysis on glucose and xylose utilization as these two sugars are the primary components in lignocellulosic biomass hydrolysate, a promising renewable carbon feedstock for industrial bioprocesses. This strain is valuable to the field as it enables the use of mixed sugar sources in traditional fed-batch based approaches, whereas the wild-type carbon catabolite repression system leads to biphasic growth and possible buildup of non-preferential sugars, reducing process efficiency at scale.
Collapse
Affiliation(s)
- Nicholas A. Kaplan
- Department of Chemical, Paper, and Biomedical Engineering, Miami University, Oxford, Ohio, USA
| | - Khondokar Nowshin Islam
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, USA
| | - Fiona C. Kanis
- Department of Chemical, Paper, and Biomedical Engineering, Miami University, Oxford, Ohio, USA
| | - Jack R. Verderber
- Department of Chemical, Paper, and Biomedical Engineering, Miami University, Oxford, Ohio, USA
| | - Xin Wang
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, USA
| | - J. Andrew Jones
- Department of Chemical, Paper, and Biomedical Engineering, Miami University, Oxford, Ohio, USA
| | - Mattheos A. G. Koffas
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York, USA
| |
Collapse
|
6
|
Aliperti L, Aptekmann AA, Farfañuk G, Couso LL, Soler-Bistué A, Sánchez IE. r/K selection of GC content in prokaryotes. Environ Microbiol 2023; 25:3255-3268. [PMID: 37813828 DOI: 10.1111/1462-2920.16511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 09/16/2023] [Indexed: 10/11/2023]
Abstract
The guanine/cytosine (GC) content of prokaryotic genomes is species-specific, taking values from 16% to 77%. This diversity of selection for GC content remains contentious. We analyse the correlations between GC content and a range of phenotypic and genotypic data in thousands of prokaryotes. GC content integrates well with these traits into r/K selection theory when phenotypic plasticity is considered. High GC-content prokaryotes are r-strategists with cheaper descendants thanks to a lower average amino acid metabolic cost, colonize unstable environments thanks to flagella and a bacillus form and are generalists in terms of resource opportunism and their defence mechanisms. Low GC content prokaryotes are K-strategists specialized for stable environments that maintain homeostasis via a high-cost outer cell membrane and endospore formation as a response to nutrient deprivation, and attain a higher nutrient-to-biomass yield. The lower proteome cost of high GC content prokaryotes is driven by the association between GC-rich codons and cheaper amino acids in the genetic code, while the correlation between GC content and genome size may be partly due to functional diversity driven by r/K selection. In all, molecular diversity in the GC content of prokaryotes may be a consequence of ecological r/K selection.
Collapse
Affiliation(s)
- Lucio Aliperti
- Facultad de Ciencias Exactas y Naturales. Laboratorio de Fisiología de Proteínas, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Ariel A Aptekmann
- Marine and Coastal Sciences Department, Rutgers University, New Brunswick, New Jersey, USA
| | - Gonzalo Farfañuk
- Facultad de Ciencias Exactas y Naturales. Laboratorio de Fisiología de Proteínas, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Luciana L Couso
- Facultad de Agronomía, Cátedra de Genética, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Alfonso Soler-Bistué
- Instituto de Investigaciones Biotecnológicas Dr. Rodolfo A. Ugalde, CONICET, Universidad Nacional de San Martín, San Martin, Argentina
| | - Ignacio E Sánchez
- Facultad de Ciencias Exactas y Naturales. Laboratorio de Fisiología de Proteínas, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Buenos Aires, Argentina
| |
Collapse
|
7
|
Madrid I, Zheng Z, Gerbelot C, Fujiwara A, Li S, Grall S, Nishiguchi K, Kim SH, Chovin A, Demaille C, Clement N. Ballistic Brownian Motion of Nanoconfined DNA. ACS NANO 2023; 17:17031-17040. [PMID: 37700490 DOI: 10.1021/acsnano.3c04349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
Theoretical treatments of polymer dynamics in liquid generally start with the basic assumption that motion at the smallest scale is heavily overdamped; therefore, inertia can be neglected. We report on the Brownian motion of tethered DNA under nanoconfinement, which was analyzed by molecular dynamics simulation and nanoelectrochemistry-based single-electron shuttle experiments. Our results show a transition into the ballistic Brownian motion regime for short DNA in sub-5 nm gaps, with quality coefficients as high as 2 for double-stranded DNA, an effect mainly attributed to a drastic increase in stiffness. The possibility for DNA to enter the underdamped regime could have profound implications on our understanding of the energetics of biomolecular engines such as the replication machinery, which operates in nanocavities that are a few nanometers wide.
Collapse
Affiliation(s)
- Ignacio Madrid
- IIS, LIMMS CNRS-IIS UMI2820, The University of Tokyo, 4-6-1 Komaba, Meguro-ku Tokyo 153-8505, Japan
| | - Zhiyong Zheng
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Cité, 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
| | - Cedric Gerbelot
- NTT Basic Research Laboratories, NTT Corporation, 3-1 Morinosato-Wakamiya, Atsugi-shi 243-0198, Japan
| | - Akira Fujiwara
- NTT Basic Research Laboratories, NTT Corporation, 3-1 Morinosato-Wakamiya, Atsugi-shi 243-0198, Japan
| | - Shuo Li
- IIS, LIMMS CNRS-IIS UMI2820, The University of Tokyo, 4-6-1 Komaba, Meguro-ku Tokyo 153-8505, Japan
| | - Simon Grall
- IIS, LIMMS CNRS-IIS UMI2820, The University of Tokyo, 4-6-1 Komaba, Meguro-ku Tokyo 153-8505, Japan
| | - Katsuhiko Nishiguchi
- NTT Basic Research Laboratories, NTT Corporation, 3-1 Morinosato-Wakamiya, Atsugi-shi 243-0198, Japan
| | - Soo Hyeon Kim
- IIS, LIMMS CNRS-IIS UMI2820, The University of Tokyo, 4-6-1 Komaba, Meguro-ku Tokyo 153-8505, Japan
| | - Arnaud Chovin
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Cité, 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
| | - Christophe Demaille
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Cité, 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
| | - Nicolas Clement
- IIS, LIMMS CNRS-IIS UMI2820, The University of Tokyo, 4-6-1 Komaba, Meguro-ku Tokyo 153-8505, Japan
- NTT Basic Research Laboratories, NTT Corporation, 3-1 Morinosato-Wakamiya, Atsugi-shi 243-0198, Japan
| |
Collapse
|
8
|
Li J, Li N, Roellig DM, Zhao W, Guo Y, Feng Y, Xiao L. High subtelomeric GC content in the genome of a zoonotic Cryptosporidium species. Microb Genom 2023; 9:mgen001052. [PMID: 37399068 PMCID: PMC10438818 DOI: 10.1099/mgen.0.001052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 05/24/2023] [Indexed: 07/04/2023] Open
Abstract
Cryptosporidium canis is a zoonotic species causing cryptosporidiosis in humans in addition to its natural hosts dogs and other fur animals. To understand the genetic basis for host adaptation, we sequenced the genomes of C. canis from dogs, minks, and foxes and conducted a comparative genomics analysis. While the genomes of C. canis have similar gene contents and organisations, they (~41.0 %) and C. felis (39.6 %) have GC content much higher than other Cryptosporidium spp. (24.3-32.9 %) sequenced to date. The high GC content is mostly restricted to subtelomeric regions of the eight chromosomes. Most of these GC-balanced genes encode Cryptosporidium-specific proteins that have intrinsically disordered regions and are involved in host-parasite interactions. Natural selection appears to play a more important role in the evolution of codon usage in GC-balanced C. canis, and most of the GC-balanced genes have undergone positive selection. While the identity in whole genome sequences between the mink- and dog-derived isolates is 99.9 % (9365 SNVs), it is only 96.0 % (362 894 SNVs) between them and the fox-derived isolate. In agreement with this, the fox-derived isolate possesses more subtelomeric genes encoding invasion-related protein families. Therefore, the change in subtelomeric GC content appears to be responsible for the more GC-balanced C. canis genomes, and the fox-derived isolate could represent a new Cryptosporidium species.
Collapse
Affiliation(s)
- Jiayu Li
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, PR China
| | - Na Li
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, PR China
| | - Dawn M. Roellig
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Wentao Zhao
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, PR China
| | - Yaqiong Guo
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, PR China
| | - Yaoyu Feng
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, PR China
| | - Lihua Xiao
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, PR China
| |
Collapse
|
9
|
Moeckel C, Zaravinos A, Georgakopoulos-Soares I. Strand Asymmetries Across Genomic Processes. Comput Struct Biotechnol J 2023; 21:2036-2047. [PMID: 36968020 PMCID: PMC10030826 DOI: 10.1016/j.csbj.2023.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/08/2023] [Accepted: 03/08/2023] [Indexed: 03/12/2023] Open
Abstract
Across biological systems, a number of genomic processes, including transcription, replication, DNA repair, and transcription factor binding, display intrinsic directionalities. These directionalities are reflected in the asymmetric distribution of nucleotides, motifs, genes, transposon integration sites, and other functional elements across the two complementary strands. Strand asymmetries, including GC skews and mutational biases, have shaped the nucleotide composition of diverse organisms. The investigation of strand asymmetries often serves as a method to understand underlying biological mechanisms, including protein binding preferences, transcription factor interactions, retrotransposition, DNA damage and repair preferences, transcription-replication collisions, and mutagenesis mechanisms. Research into this subject also enables the identification of functional genomic sites, such as replication origins and transcription start sites. Improvements in our ability to detect and quantify DNA strand asymmetries will provide insights into diverse functionalities of the genome, the contribution of different mutational mechanisms in germline and somatic mutagenesis, and our knowledge of genome instability and evolution, which all have significant clinical implications in human disease, including cancer. In this review, we describe key developments that have been made across the field of genomic strand asymmetries, as well as the discovery of associated mechanisms.
Collapse
Affiliation(s)
- Camille Moeckel
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Apostolos Zaravinos
- Department of Life Sciences, European University Cyprus, Diogenis Str., 6, Nicosia 2404, Cyprus
- Cancer Genetics, Genomics and Systems Biology laboratory, Basic and Translational Cancer Research Center (BTCRC), Nicosia 1516, Cyprus
- Corresponding author at: Department of Life Sciences, European University Cyprus, Diogenis Str., 6, Nicosia 2404, Cyprus.
| | - Ilias Georgakopoulos-Soares
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
- Corresponding author.
| |
Collapse
|
10
|
Pu F, Wang R, Yang X, Hu X, Wang J, Zhang L, Zhao Y, Zhang D, Liu Z, Liu J. Nucleotide and codon usage biases involved in the evolution of African swine fever virus: A comparative genomics analysis. J Basic Microbiol 2023; 63:499-518. [PMID: 36782108 DOI: 10.1002/jobm.202200624] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/05/2023] [Accepted: 01/21/2023] [Indexed: 02/15/2023]
Abstract
Since African swine fever virus (ASFV) replication is closely related to its host's machinery, codon usage of viral genome can be subject to selection pressures. A better understanding of codon usage can give new insights into viral evolution. We implemented information entropy and revealed that the nucleotide usage pattern of ASFV is significantly associated with viral isolation factors (region and time), especially the usages of thymine and cytosine. Despite the domination of adenine and thymine in the viral genome, we found that mutation pressure alters the overall codon usage pattern of ASFV, followed by selective forces from natural selection. Moreover, the nucleotide skew index at the gene level indicates that nucleotide usages influencing synonymous codon bias of ASFV are significantly correlated with viral protein hydropathy. Finally, evolutionary plasticity is proved to contribute to the weakness in synonymous codons with A- or T-end serving as optimal codons of ASFV, suggesting that fine-tuning translation selection plays a role in synonymous codon usages of ASFV for adapting host. Taken together, ASFV is subject to evolutionary dynamics on nucleotide selections and synonymous codon usage, and our detailed analysis offers deeper insights into the genetic characteristics of this newly emerging virus around the world.
Collapse
Affiliation(s)
- Feiyang Pu
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Rui Wang
- Viterbi School of Engineering, University of Southern California, Los Angeles, California, USA
| | - Xuanye Yang
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Xinyan Hu
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Jinqian Wang
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Lijuan Zhang
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Yongqing Zhao
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Derong Zhang
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Zewen Liu
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Junlin Liu
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| |
Collapse
|
11
|
Shi F, Yu T, Xu Y, Zhang S, Niu Y, Ge S, Tao J, Zong S. Comparative mitochondrial genomic analysis provides new insights into the evolution of the subfamily Lamiinae (Coleoptera: Cerambycidae). Int J Biol Macromol 2023; 225:634-647. [PMID: 36403761 DOI: 10.1016/j.ijbiomac.2022.11.125] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 10/23/2022] [Accepted: 11/12/2022] [Indexed: 11/18/2022]
Abstract
The genus Monochamus within the subfamily Lamiinae is the main vector of Bursaphelenchus xylophilus, which causes pine wilt disease and induces substantial economic and ecological losses. Only three complete mitochondrial genomes of the genus Monochamus have been sequenced to date, and no comparative mitochondrial genomic studies of Lamiinae have been conducted. Here, the mitochondrial genomes of two Monochamus species, M. saltuarius and M. urussovi, were newly sequenced and annotated. The composition and order of genes in the mitochondrial genomes of Monochamus species are conserved. All transfer RNAs exhibit the typical clover-leaf secondary structure, with the exception of trnS1. Similar to other longhorn beetles, Lamiinae mitochondrial genomes have an A + T bias. All 13 protein-coding genes have experienced purifying selection, and tandem repeat sequences are abundant in the A + T-rich region. Phylogenetic analyses revealed congruent topologies among trees inferred from the five datasets, with the monophyly of Acanthocinini, Agapanthiini, Batocerini, Dorcaschematini, Pteropliini, and Saperdini receiving high support. The findings of this study enhance our understanding of mitochondrial genome evolution and will provide a basis for future studies of population genetics and phylogenetic investigations in this group.
Collapse
Affiliation(s)
- Fengming Shi
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing 100083, China.
| | - Tao Yu
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insect of the Mountainous Region, Guiyang University, Guiyang 550005, China.
| | - Yabei Xu
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing 100083, China.
| | - Sainan Zhang
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing 100083, China.
| | - Yiming Niu
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing 100083, China.
| | - Sixun Ge
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing 100083, China.
| | - Jing Tao
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing 100083, China.
| | - Shixiang Zong
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing 100083, China.
| |
Collapse
|
12
|
The Mitochondrial Genome of the Globally Invasive Barnacle Megabalanus coccopoma Darwin 1854 (Crustacea: Balanomorpha): Rearrangement and Phylogenetic Consideration within Balanomorpha. DIVERSITY 2023. [DOI: 10.3390/d15010117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Megabalanus coccopoma (Darwin, 1854) is a globally invasive species in Balanomorpha (Crustacea). This species is a model organism for studying marine pollution and ecology. However, its mitogenome remains unknown. The mitogenome sequencing of M. coccopoma is completed in the present study. It has a 15,098 bp in length, including 13 protein-coding genes (PCGs), 2 ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs), along with a putative regulatory area. A substantial A+T bias was observed in the genome composition (68.2%), along with a negative AT (0.82) and GC (−0.136) skew. Compared to the gene sequence of the ground model of pan-crustacea, 13 gene clusters (or genes), such as 10 tRNAs and 3 PCGs, were observed in a different order. This was in line with the previously observed large-scale gene rearrangements of Balanomorpha. Among the 37 genes, the gene cluster (M-nad2-W-cox1-L2-cox2-D-atp8-atp6-cox3-G- nad3-R-N-A-E-S1) Balanomorpha was conserved. Furthermore, phylogeny analysis indicated that the existing Balanomorpha species family was divided into nine rearrangement patterns, supporting the polyphyly of Balanoidea.
Collapse
|
13
|
Dong MJ, Luo H, Gao F. DoriC 12.0: an updated database of replication origins in both complete and draft prokaryotic genomes. Nucleic Acids Res 2022; 51:D117-D120. [PMID: 36305822 PMCID: PMC9825612 DOI: 10.1093/nar/gkac964] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/08/2022] [Accepted: 10/13/2022] [Indexed: 01/29/2023] Open
Abstract
DoriC was first launched in 2007 as a database of replication origins (oriCs) in bacterial genomes and has since been constantly updated to integrate the latest research progress in this field. The database was subsequently extended to include the oriCs in archaeal genomes as well as those in plasmids. This latest release, DoriC 12.0, includes the oriCs in both draft and complete prokaryotic genomes. At the same time, the number of oriCs in the database has also increased significantly and currently contains over 200 000 bacterial entries distributed in more than 40 phyla. Among them, a large number are from bacteria in new phyla whose oriCs were not explored before. Additionally, new oriC features and improvements have been introduced, especially in the visualization and analysis of oriCs. Currently, DoriC is considered as an important database in the fields of bioinformatics, microbial genomics, and even synthetic biology, providing a valuable resource as well as a comprehensive platform for the research on oriCs. DoriC 12.0 can be accessed at https://tubic.org/doric/ and http://tubic.tju.edu.cn/doric/.
Collapse
Affiliation(s)
| | | | - Feng Gao
- To whom correspondence should be addressed. Tel: +86 22 27404118; Fax: +86 22 27404118;
| |
Collapse
|
14
|
Dong MJ, Luo H, Gao F. Ori-Finder 2022: A Comprehensive Web Server for Prediction and Analysis of Bacterial Replication Origins. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:1207-1213. [PMID: 36257484 DOI: 10.1016/j.gpb.2022.10.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 09/21/2022] [Accepted: 10/11/2022] [Indexed: 12/26/2022]
Abstract
The replication of DNA is a complex biological process that is essential for life. Bacterial DNA replication is initiated at genomic loci referred to as replication origins (oriCs). Integrating the Z-curve method, DnaA box distribution, and comparative genomic analysis, we developed a web server to predict bacterial oriCs in 2008 called Ori-Finder, which contributes to clarify the characteristics of bacterial oriCs. The oriCs of hundreds of sequenced bacterial genomes have been annotated in the genome reports using Ori-Finder and the predicted results have been deposited in DoriC, a manually curated database of oriCs. This has facilitated large-scale data mining of functional elements in oriCs and strand-biased analysis. Here, we describe Ori-Finder 2022 with updated prediction framework, interactive visualization module, new analysis module, and user-friendly interface. More species-specific indicator genes and functional elements of oriCs are integrated into the updated framework, which has also been redesigned to predict oriCs in draft genomes. The interactive visualization module displays more genomic information related to oriCs and their functional elements. The analysis module includes regulatory protein annotation, repeat sequence discovery, homologous oriC search, and strand-biased analyses. The redesigned interface provides additional customization options for oriC prediction. Ori-Finder 2022 is freely available at http://tubic.tju.edu.cn/Ori-Finder/ and https://tubic.org/Ori-Finder/.
Collapse
Affiliation(s)
- Mei-Jing Dong
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
| | - Hao Luo
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
| | - Feng Gao
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China; Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China.
| |
Collapse
|
15
|
Yang Y, Kang Y, Tong J, Ge X, Yang X, Liu H. Mitochondrial gene rearrangements suggest a new genus in the subfamily Cantharinae (Coleoptera). ZOOL SCR 2022. [DOI: 10.1111/zsc.12572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yuxia Yang
- Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development Hebei University Baoding China
| | - Ya Kang
- Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development Hebei University Baoding China
| | - Junbo Tong
- Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development Hebei University Baoding China
| | - Xueying Ge
- Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development Hebei University Baoding China
| | - Xingke Yang
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology, Chinese Academy of Sciences Beijing China
| | - Haoyu Liu
- Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development Hebei University Baoding China
| |
Collapse
|
16
|
Complete Mitogenomes of Polypedates Tree Frogs Unveil Gene Rearrangement and Concerted Evolution within Rhacophoridae. Animals (Basel) 2022; 12:ani12182449. [PMID: 36139309 PMCID: PMC9494961 DOI: 10.3390/ani12182449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 09/10/2022] [Accepted: 09/13/2022] [Indexed: 11/28/2022] Open
Abstract
Simple Summary Duplicated control regions have been reported several times in the tree frog family Rhacophoridae, and previous studies have mostly relied on sequence analysis to reconstruct their evolution. This is the first study to employ a phylogenetic method to demonstrate the existence of concerted and parallel evolution succinctly and intuitively in the duplicated control regions of the family Rhacophoridae. Phylogenetic relationships were also used to illustrate the parallel evolution of ATP8 loss of function in the genus Polypedates. In general, this study elucidated the evolutionary patterns and pathways of mitochondrial gene rearrangement of the family Rhacophoridae from a phylogenetic perspective, which aids in understanding the evolutionary history of this fascinating tree frog taxon from a molecular evolution standpoint. Abstract New developments in sequencing technology and nucleotide analysis have allowed us to make great advances in reconstructing anuran phylogeny. As a clade of representative amphibians that have radiated from aquatic to arboreal habitats, our understanding of the systematic status and molecular biology of rhacophorid tree frogs is still limited. We determined two new mitogenomes for the genus Polypedates (Rhacophoridae): P. impresus and P. mutus. We conducted comparative and phylogenetic analyses using our data and seven other rhacophorid mitogenomes. The mitogenomes of the genera Polypedates, Buergeria, and Zhangixalus were almost identical, except that the ATP8 gene in Polypedates had become a non-coding region; Buergeria maintained the legacy “LTPF” tRNA gene cluster compared to the novel “TLPF” order in the other two genera; and B. buergeri and Z. dennysi had no control region (CR) duplication. The resulting phylogenetic relationship supporting the above gene rearrangement pathway suggested parallel evolution of ATP8 gene loss of function (LoF) in Polypedates and CR duplication with concerted evolution of paralogous CRs in rhacophorids. Finally, conflicting topologies in the phylograms of 185 species reflected the advantages of phylogenetic analyses using multiple loci.
Collapse
|
17
|
Bharti R, Siebert D, Blombach B, Grimm DG. Systematic analysis of the underlying genomic architecture for transcriptional-translational coupling in prokaryotes. NAR Genom Bioinform 2022; 4:lqac074. [PMID: 36186922 PMCID: PMC9514032 DOI: 10.1093/nargab/lqac074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 09/05/2022] [Accepted: 09/15/2022] [Indexed: 11/12/2022] Open
Abstract
Transcriptional-translational coupling is accepted to be a fundamental mechanism of gene expression in prokaryotes and therefore has been analyzed in detail. However, the underlying genomic architecture of the expression machinery has not been well investigated so far. In this study, we established a bioinformatics pipeline to systematically investigated >1800 bacterial genomes for the abundance of transcriptional and translational associated genes clustered in distinct gene cassettes. We identified three highly frequent cassettes containing transcriptional and translational genes, i.e. rplk-nusG (gene cassette 1; in 553 genomes), rpoA-rplQ-rpsD-rpsK-rpsM (gene cassette 2; in 656 genomes) and nusA-infB (gene cassette 3; in 877 genomes). Interestingly, each of the three cassettes harbors a gene (nusG, rpsD and nusA) encoding a protein which links transcription and translation in bacteria. The analyses suggest an enrichment of these cassettes in pathogenic bacterial phyla with >70% for cassette 3 (i.e. Neisseria, Salmonella and Escherichia) and >50% for cassette 1 (i.e. Treponema, Prevotella, Leptospira and Fusobacterium) and cassette 2 (i.e. Helicobacter, Campylobacter, Treponema and Prevotella). These insights form the basis to analyze the transcriptional regulatory mechanisms orchestrating transcriptional-translational coupling and might open novel avenues for future biotechnological approaches.
Collapse
Affiliation(s)
- Richa Bharti
- Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Bioinformatics, Petersgasse 18, 94315 Straubing, Germany
- Weihenstephan-Triesdorf University of Applied Sciences, Petersgasse 18, 94315 Straubing, Germany
- SynBiofoundry@TUM, Technical University of Munich, Schulgasse 22, 94315 Straubing, Germany
| | - Daniel Siebert
- SynBiofoundry@TUM, Technical University of Munich, Schulgasse 22, 94315 Straubing, Germany
- Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Microbial Biotechnology, Uferstraße 53, 94315 Straubing, Germany
| | - Bastian Blombach
- SynBiofoundry@TUM, Technical University of Munich, Schulgasse 22, 94315 Straubing, Germany
- Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Microbial Biotechnology, Uferstraße 53, 94315 Straubing, Germany
| | - Dominik G Grimm
- Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Bioinformatics, Petersgasse 18, 94315 Straubing, Germany
- Weihenstephan-Triesdorf University of Applied Sciences, Petersgasse 18, 94315 Straubing, Germany
- SynBiofoundry@TUM, Technical University of Munich, Schulgasse 22, 94315 Straubing, Germany
- Technical University of Munich, Department of Informatics, Boltzmannstr. 3, 85748 Garching, Germany
| |
Collapse
|
18
|
Mitochondrial Genomes Provide New Phylogenetic and Evolutionary Insights into Psilidae (Diptera: Brachycera). INSECTS 2022; 13:insects13060518. [PMID: 35735855 PMCID: PMC9224655 DOI: 10.3390/insects13060518] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 05/29/2022] [Accepted: 05/30/2022] [Indexed: 02/05/2023]
Abstract
Psilidae (Diptera: Brachycera) is a moderate-sized family currently placed in the superfamily Diopsoidea and contains some destructive agricultural and forestry pests. The systematic position and intrafamilial classification of rust flies are in need of further study, and the available molecular data of Psilidae are still limited. In this study, we present the mitochondrial genomes of 6 Psilidae species (Chamaepsilatestudinaria Wang and Yang, Chyliza bambusae Wang and Yang, Chy. chikuni Wang, Loxocera lunata Wang and Yang, L. planivena Wang and Yang and L. sinica Wang and Yang). Comparative analyses show a conserved genome structure, in terms of gene composition and arrangement, and a highly Adenine plus Thymine biased nucleotide composition of the 6 psilid mitogenomes. Mitochondrial evolutionary rates vary among the 6 species, with species of Chylizinae exhibiting a slower average rate than species of Psilinae. The length, the nucleotide composition, and the copy number of repeat units of the control region are variable among the 6 species, which may offer useful information for phylogenetic and evolutionary studies of Psilidae. Phylogenetic analyses based on 4 mitogenomic datasets (AA, PCG, PCG12RNA, and PCGRNA) support the monophyly of Psilidae, and the sister relationship between Chylizinae and Psilinae, while Diopsoidea is suggested to be non-monophyletic. Our study enlightens the future application of mitogenomic data in the phylogenetic and evolutionary studies of Psilidae, based on denser taxon sampling.
Collapse
|
19
|
Consistent Clustering Pattern of Prokaryotic Genes Based on Base Frequency at the Second Codon Position and its Association with Functional Category Preference. Interdiscip Sci 2022; 14:349-357. [PMID: 34817803 PMCID: PMC9124167 DOI: 10.1007/s12539-021-00493-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 11/02/2021] [Accepted: 11/07/2021] [Indexed: 10/26/2022]
Abstract
AbstractIn 2002, our research group observed a gene clustering pattern based on the base frequency of A versus T at the second codon position in the genome of Vibrio cholera and found that the functional category distribution of genes in the two clusters was different. With the availability of a large number of sequenced genomes, we performed a systematic investigation of A2–T2 distribution and found that 2694 out of 2764 prokaryotic genomes have an optimal clustering number of two, indicating a consistent pattern. Analysis of the functional categories of the coding genes in each cluster in 1483 prokaryotic genomes indicated, that 99.33% of the genomes exhibited a significant difference (p < 0.01) in function distribution between the two clusters. Specifically, functional category P was overrepresented in the small cluster of 98.65% of genomes, whereas categories J, K, and L were overrepresented in the larger cluster of over 98.52% of genomes. Lineage analysis uncovered that these preferences appear consistently across all phyla. Overall, our work revealed an almost universal clustering pattern based on the relative frequency of A2 versus T2 and its role in functional category preference. These findings will promote the understanding of the rationality of theoretical prediction of functional classes of genes from their nucleotide sequences and how protein function is determined by DNA sequence.
Graphical abstract
Collapse
|
20
|
Jin YT, Pu DK, Guo HX, Deng Z, Chen LL, Guo FB. T-G-A Deficiency Pattern in Protein-Coding Genes and Its Potential Reason. Front Microbiol 2022; 13:847325. [PMID: 35602045 PMCID: PMC9116502 DOI: 10.3389/fmicb.2022.847325] [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: 01/02/2022] [Accepted: 03/30/2022] [Indexed: 11/20/2022] Open
Abstract
If a stop codon appears within one gene, then its translation will be terminated earlier than expected. False folding of premature protein will be adverse to the host; hence, all functional genes would tend to avoid the intragenic stop codons. Therefore, we hypothesize that there will be less frequency of nucleotides corresponding to stop codons at each codon position of genes. Here, we validate this inference by investigating the nucleotide frequency at a large scale and results from 19,911 prokaryote genomes revealed that nucleotides coinciding with stop codons indeed have the lowest frequency in most genomes. Interestingly, genes with three types of stop codons all tend to follow a T-G-A deficiency pattern, suggesting that the property of avoiding intragenic termination pressure is the same and the major stop codon TGA plays a dominant role in this effect. Finally, a positive correlation between the TGA deficiency extent and the base length was observed in start-experimentally verified genes of Escherichia coli (E. coli). This strengthens the proof of our hypothesis. The T-G-A deficiency pattern observed would help to understand the evolution of codon usage tactics in extant organisms.
Collapse
Affiliation(s)
- Yan-Ting Jin
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China.,Department of Respiratory and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Dong-Kai Pu
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Hai-Xia Guo
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Zixin Deng
- Department of Respiratory and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Ling-Ling Chen
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Feng-Biao Guo
- Department of Respiratory and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| |
Collapse
|
21
|
Merrikh H, Merrikh C. Reply to: Testing the adaptive hypothesis of lagging-strand encoding in bacterial genomes. Nat Commun 2022; 13:2627. [PMID: 35551437 PMCID: PMC9098457 DOI: 10.1038/s41467-022-30014-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 03/08/2022] [Indexed: 11/09/2022] Open
Affiliation(s)
- Houra Merrikh
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA.
| | | |
Collapse
|
22
|
Liu H, Zhang J. Testing the adaptive hypothesis of lagging-strand encoding in bacterial genomes. Nat Commun 2022; 13:2628. [PMID: 35552380 PMCID: PMC9098844 DOI: 10.1038/s41467-022-30000-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 04/12/2021] [Indexed: 11/24/2022] Open
Affiliation(s)
- Haoxuan Liu
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, United States
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, United States.
| |
Collapse
|
23
|
Markosian C, Staquicini DI, Dogra P, Dodero-Rojas E, Lubin JH, Tang FH, Smith TL, Contessoto VG, Libutti SK, Wang Z, Cristini V, Khare SD, Whitford PC, Burley SK, Onuchic JN, Pasqualini R, Arap W. Genetic and Structural Analysis of SARS-CoV-2 Spike Protein for Universal Epitope Selection. Mol Biol Evol 2022; 39:msac091. [PMID: 35511693 PMCID: PMC9129195 DOI: 10.1093/molbev/msac091] [Citation(s) in RCA: 2] [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] [Indexed: 11/14/2022] Open
Abstract
Evaluation of immunogenic epitopes for universal vaccine development in the face of ongoing SARS-CoV-2 evolution remains a challenge. Herein, we investigate the genetic and structural conservation of an immunogenically relevant epitope (C662-C671) of spike (S) protein across SARS-CoV-2 variants to determine its potential utility as a broad-spectrum vaccine candidate against coronavirus diseases. Comparative sequence analysis, structural assessment, and molecular dynamics simulations of C662-C671 epitope were performed. Mathematical tools were employed to determine its mutational cost. We found that the amino acid sequence of C662-C671 epitope is entirely conserved across the observed major variants of SARS-CoV-2 in addition to SARS-CoV. Its conformation and accessibility are predicted to be conserved, even in the highly mutated Omicron variant. Costly mutational rate in the context of energy expenditure in genome replication and translation can explain this strict conservation. These observations may herald an approach to developing vaccine candidates for universal protection against emergent variants of coronavirus.
Collapse
Affiliation(s)
- Christopher Markosian
- Rutgers Cancer Institute of New Jersey, Newark, NJ 07101, USA
- Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| | - Daniela I. Staquicini
- Rutgers Cancer Institute of New Jersey, Newark, NJ 07101, USA
- Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| | - Prashant Dogra
- Mathematics in Medicine Program, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10022, USA
| | - Esteban Dodero-Rojas
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
| | - Joseph H. Lubin
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Fenny H.F. Tang
- Rutgers Cancer Institute of New Jersey, Newark, NJ 07101, USA
- Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| | - Tracey L. Smith
- Rutgers Cancer Institute of New Jersey, Newark, NJ 07101, USA
- Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| | | | - Steven K. Libutti
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
- Department of Surgery, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ 08901, USA
| | - Zhihui Wang
- Mathematics in Medicine Program, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10022, USA
| | - Vittorio Cristini
- Mathematics in Medicine Program, Houston Methodist Research Institute, Houston, TX 77030, USA
- Neal Cancer Center, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Imaging Physics, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
- Physiology, Biophysics, and Systems Biology Program, Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY 10022, USA
| | - Sagar D. Khare
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Paul C. Whitford
- Department of Physics and Center for Theoretical Biological Physics, Northeastern University, Boston, MA 02115, USA
| | - Stephen K. Burley
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- RCSB Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- RCSB Protein Data Bank, San Diego Supercomputer Center, and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92067, USA
| | - José N. Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- Department of Biosciences, Rice University, Houston, TX 77005, USA
- Department of Chemistry, Rice University, Houston, TX 77005, USA
- Department of Physics and Astronomy, Rice University, Houston, TX 77005, USA
| | - Renata Pasqualini
- Rutgers Cancer Institute of New Jersey, Newark, NJ 07101, USA
- Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| | - Wadih Arap
- Rutgers Cancer Institute of New Jersey, Newark, NJ 07101, USA
- Division of Hematology/Oncology, Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| |
Collapse
|
24
|
Yuan L, Liu H, Ge X, Yang G, Xie G, Yang Y. A Mitochondrial Genome Phylogeny of Cleridae (Coleoptera, Cleroidea). INSECTS 2022; 13:insects13020118. [PMID: 35206692 PMCID: PMC8878092 DOI: 10.3390/insects13020118] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/16/2022] [Accepted: 01/19/2022] [Indexed: 01/22/2023]
Abstract
The predaceous beetle family Cleridae includes a large and widely distributed rapid radiation, which is vital for the ecosystem. Despite its important role, a number of problems remain to be solved regarding the phylogenetic inter-relationships, the timing of divergence, and the mitochondrial biology. Mitochondrial genomes have been widely used to reconstruct phylogenies of various insect groups, but never introduced to Cleridae until now. Here, we generated 18 mitochondrial genomes to address these issues, which are all novel to the family. In addition to phylogenomic analysis, we have leveraged our new sources to study the mitochondrial biology in terms of nucleotide composition, codon usage and substitutional rate, to understand how these vital cellular components may have contributed to the divergence of the Cleridae. Our results recovered Korynetinae sister to the remaining clerids, and the calde of Clerinae+Hydnocerinae is indicated more related to Tillinae. A time-calibrated phylogeny estimated the earliest divergence time of Cleridae was soon after the origin of the family, not later than 160.18 Mya (95% HPD: 158.18–162.07 Mya) during the mid-Jurassic. This is the first mitochondrial genome-based phylogenetic study of the Cleridae that covers nearly all subfamily members, which provides an alternative evidence for reconstructing the phylogenetic relationships.
Collapse
Affiliation(s)
- Lilan Yuan
- The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (L.Y.); (X.G.)
- College of Agriculture, Yangtze University, Jingzhou 434025, China;
| | - Haoyu Liu
- The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (L.Y.); (X.G.)
- Correspondence: (H.L.); (Y.Y.)
| | - Xueying Ge
- The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (L.Y.); (X.G.)
| | - Ganyan Yang
- Beijing Dabu Biotechnology Service Co., Ltd., Beijing 100085, China;
| | - Guanglin Xie
- College of Agriculture, Yangtze University, Jingzhou 434025, China;
| | - Yuxia Yang
- The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (L.Y.); (X.G.)
- Correspondence: (H.L.); (Y.Y.)
| |
Collapse
|
25
|
Cost-Efficiency Optimization Serves as a Conserved Mechanism that Promotes Osteosarcoma in Mammals. J Mol Evol 2022; 90:139-148. [DOI: 10.1007/s00239-022-10047-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 01/06/2022] [Indexed: 10/19/2022]
|
26
|
Kelly S. The economics of organellar gene loss and endosymbiotic gene transfer. Genome Biol 2021; 22:345. [PMID: 34930424 PMCID: PMC8686548 DOI: 10.1186/s13059-021-02567-w] [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: 09/09/2021] [Accepted: 12/06/2021] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND The endosymbiosis of the bacterial progenitors of the mitochondrion and the chloroplast are landmark events in the evolution of life on Earth. While both organelles have retained substantial proteomic and biochemical complexity, this complexity is not reflected in the content of their genomes. Instead, the organellar genomes encode fewer than 5% of the genes found in living relatives of their ancestors. While many of the 95% of missing organellar genes have been discarded, others have been transferred to the host nuclear genome through a process known as endosymbiotic gene transfer. RESULTS Here, we demonstrate that the difference in the per-cell copy number of the organellar and nuclear genomes presents an energetic incentive to the cell to either delete organellar genes or transfer them to the nuclear genome. We show that, for the majority of transferred organellar genes, the energy saved by nuclear transfer exceeds the costs incurred from importing the encoded protein into the organelle where it can provide its function. Finally, we show that the net energy saved by endosymbiotic gene transfer can constitute an appreciable proportion of total cellular energy budgets and is therefore sufficient to impart a selectable advantage to the cell. CONCLUSION Thus, reduced cellular cost and improved energy efficiency likely played a role in the reductive evolution of mitochondrial and chloroplast genomes and the transfer of organellar genes to the nuclear genome.
Collapse
Affiliation(s)
- Steven Kelly
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK.
| |
Collapse
|
27
|
A novel statistical method predicts mutability of the genomic segments of the SARS-CoV-2 virus. QRB DISCOVERY 2021; 3:e1. [PMID: 35106478 PMCID: PMC8795775 DOI: 10.1017/qrd.2021.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 05/28/2021] [Accepted: 11/26/2021] [Indexed: 11/06/2022] Open
Abstract
Abstract
The SARS-CoV-2 virus has made the largest pandemic of the 21st century, with hundreds of millions of cases and tens of millions of fatalities. Scientists all around the world are racing to develop vaccines and new pharmaceuticals to overcome the pandemic and offer effective treatments for COVID-19 disease. Consequently, there is an essential need to better understand how the pathogenesis of SARS-CoV-2 is affected by viral mutations and to determine the conserved segments in the viral genome that can serve as stable targets for novel therapeutics. Here, we introduce a text-mining method to estimate the mutability of genomic segments directly from a reference (ancestral) whole genome sequence. The method relies on calculating the importance of genomic segments based on their spatial distribution and frequency over the whole genome. To validate our approach, we perform a large-scale analysis of the viral mutations in nearly 80,000 publicly available SARS-CoV-2 predecessor whole genome sequences and show that these results are highly correlated with the segments predicted by the statistical method used for keyword detection. Importantly, these correlations are found to hold at the codon and gene levels, as well as for gene coding regions. Using the text-mining method, we further identify codon sequences that are potential candidates for siRNA-based antiviral drugs. Significantly, one of the candidates identified in this work corresponds to the first seven codons of an epitope of the spike glycoprotein, which is the only SARS-CoV-2 immunogenic peptide without a match to a human protein.
Collapse
|
28
|
High-Fructose Diet Alters Intestinal Microbial Profile and Correlates with Early Tumorigenesis in a Mouse Model of Barrett’s Esophagus. Microorganisms 2021; 9:microorganisms9122432. [PMID: 34946037 PMCID: PMC8708753 DOI: 10.3390/microorganisms9122432] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 12/12/2022] Open
Abstract
Esophageal adenocarcinoma (EAC) is mostly prevalent in industrialized countries and has been associated with obesity, commonly linked with a diet rich in fat and refined sugars containing high fructose concentrations. In meta-organisms, dietary components are digested and metabolized by the host and its gut microbiota. Fructose has been shown to induce proliferation and cell growth in pancreas and colon cancer cell lines and also alter the gut microbiota. In a previous study with the L2-IL-1B mouse model, we showed that a high-fat diet (HFD) accelerated EAC progression from its precursor lesion Barrett’s esophagus (BE) through changes in the gut microbiota. Aiming to investigate whether a high-fructose diet (HFrD) also alters the gut microbiota and favors EAC carcinogenesis, we assessed the effects of HFrD on the phenotype and intestinal microbial communities of L2-IL1B mice. Results showed a moderate acceleration in histologic disease progression, a mild effect on the systemic inflammatory response, metabolic changes in the host, and a shift in the composition, metabolism, and functionality of intestinal microbial communities. We conclude that HFrD alters the overall balance of the gut microbiota and induces an acceleration in EAC progression in a less pronounced manner than HFD.
Collapse
|
29
|
Comparative Analysis of Eight Mitogenomes of Bark Beetles and Their Phylogenetic Implications. INSECTS 2021; 12:insects12100949. [PMID: 34680718 PMCID: PMC8538572 DOI: 10.3390/insects12100949] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 11/23/2022]
Abstract
Simple Summary Many bark beetles are destructive pests in coniferous forests and cause extensive ecological and economic losses worldwide. Comparative studies of the structural characteristics of mitogenomes and phylogenetic relationships of bark beetles can improve our understanding of mitogenome evolution. In this study, we sequenced eight mitogenomes of bark beetles. Our results show that the use of start and stop codons, the abundance of amino acids, and the relative frequency of codon use are conserved among the eight bark beetles. Different regions of tRNA exhibit different degrees of conservatism. Together with the analysis of evolutionary rates and genetic distance among bark beetle species, our results reveal phylogenetic relationships among bark beetles of the subfamily Scolytinae. Abstract Many bark beetles of the subfamily Scolytinae are the most economically important insect pests of coniferous forests worldwide. In this study, we sequenced the mitochondrial genomes of eight bark beetle species, including Dendroctonus micans, Orthotomicus erosus, Polygraphus poligraphus, Dryocoetes hectographus, Ips nitidus, Ips typographus, Ips subelongatus, and Ips hauseri, to examine their structural characteristics and determine their phylogenetic relationships. We also used previously published mitochondrial genome sequence data from other Scolytinae species to identify and localize the eight species studied within the bark beetle phylogeny. Their gene arrangement matched the presumed ancestral pattern of these bark beetles. Start and stop codon usage, amino acid abundance, and the relative codon usage frequencies were conserved among bark beetles. Genetic distances between species ranged from 0.037 to 0.418, and evolutionary rates of protein-coding genes ranged from 0.07 for COI to 0.69 for ND2. Our results shed light on the phylogenetic relationships and taxonomic status of several bark beetles in the subfamily Scolytinae and highlight the need for further sequencing analyses and taxonomic revisions in additional bark beetle species.
Collapse
|
30
|
Markosian C, Staquicini DI, Dogra P, Dodero-rojas E, Tang FHF, Smith TL, Contessoto VG, Libutti SK, Wang Z, Cristini V, Whitford PC, Burley SK, Onuchic JN, Pasqualini R, Arap W. Apropos of Universal Epitope Discovery for COVID-19 Vaccines: A Framework for Targeted Phage Display-Based Delivery and Integration of New Evaluation Tools.. [PMID: 34676381 PMCID: PMC8529634 DOI: 10.1101/2021.08.30.458222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Targeted bacteriophage (phage) particles are potentially attractive yet inexpensive platforms for immunization. Herein, we describe targeted phage capsid display of an immunogenically relevant epitope of the SARS-CoV-2 Spike protein that is empirically conserved, likely due to the high mutational cost among all variants identified to date. This observation may herald an approach to developing vaccine candidates for broad-spectrum, towards universal, protection against multiple emergent variants of coronavirus that cause COVID-19.
Collapse
|
31
|
Yu Y, Li Y, Dong Y, Wang X, Li C, Jiang W. Natural selection on synonymous mutations in SARS-CoV-2 and the impact on estimating divergence time. Future Virol 2021. [PMCID: PMC8132620 DOI: 10.2217/fvl-2021-0078] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
To adapt to human host environment, synonymous mutations in SARS-CoV-2 are shaped by tRNA selection, energy cost and RNA structure.
Collapse
Affiliation(s)
- Yuanyuan Yu
- Department of Anesthesiology, Qingdao Haici Hospital, Qingdao, Shandong, China
| | - Yan Li
- Department of Cardiology, Qingdao Center Hospital, Qingdao, Shandong, China
| | - Yu Dong
- Department of Intervention, Qingdao Center Hospital, Qingdao, Shandong, China
| | - Xuekun Wang
- Department of Cardiology, Qingdao Center Hospital, Qingdao, Shandong, China
| | - Chunxiao Li
- Department of Cardiology, Qingdao Center Hospital, Qingdao, Shandong, China
| | - Wenqing Jiang
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, Shandong, China
| |
Collapse
|
32
|
Ge X, Yuan L, Kang Y, Liu T, Liu H, Yang Y. Characterization of the First Complete Mitochondrial Genome of Cyphonocerinae (Coleoptera: Lampyridae) with Implications for Phylogeny and Evolution of Fireflies. INSECTS 2021; 12:570. [PMID: 34206376 PMCID: PMC8307346 DOI: 10.3390/insects12070570] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/11/2021] [Accepted: 06/19/2021] [Indexed: 11/16/2022]
Abstract
Complete mitochondrial genomes are valuable resources for phylogenetics in insects. The Cyphonoceridae represents an important lineage of fireflies. However, no complete mitogenome is available until now. Here, the first complete mitochondrial genome from this subfamily was reported, with Cyphonocerus sanguineus klapperichi as a representative. The mitogenome of C. sanguineus klapperichi was conserved in the structure and comparable to that of others in size and A+T content. Nucleotide composition was A+T-biased, and all genes exhibited a positive AT-skew and negative GC-skew. Two types of tandem repeat sequence units were present in the control region (136 bp × 2; 171 bp × 2 + 9 bp). For reconstruction of Lampyridae's phylogeny, three different datasets were analyzed by both maximum likelihood (ML) and Bayesian inference (BI) methods. As a result, the same topology was produced by both ML analysis of 13 protein-coding genes and 2rRNA and BI analysis of 37 genes. The results indicated that Lampyridae, Lampyrinae, Luciolinae (excluding Emeia) were monophyletic, but Ototretinae was paraphyletic, of which Stenocladius was recovered as the sister taxon to all others, while Drilaster was more closely related to Cyphonocerinae; Phturinae + Emeia were included in a monophyletic clade, which comprised sister groups with Lampyridae. Vesta was deeply rooted in the Luciolinae.
Collapse
Affiliation(s)
- Xueying Ge
- The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (X.G.); (L.Y.); (Y.K.); (T.L.)
| | - Lilan Yuan
- The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (X.G.); (L.Y.); (Y.K.); (T.L.)
- College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Ya Kang
- The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (X.G.); (L.Y.); (Y.K.); (T.L.)
| | - Tong Liu
- The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (X.G.); (L.Y.); (Y.K.); (T.L.)
| | - Haoyu Liu
- The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (X.G.); (L.Y.); (Y.K.); (T.L.)
| | - Yuxia Yang
- The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (X.G.); (L.Y.); (Y.K.); (T.L.)
| |
Collapse
|
33
|
Veldsman WP, Ma KY, Hui JHL, Chan TF, Baeza JA, Qin J, Chu KH. Comparative genomics of the coconut crab and other decapod crustaceans: exploring the molecular basis of terrestrial adaptation. BMC Genomics 2021; 22:313. [PMID: 33931033 PMCID: PMC8086120 DOI: 10.1186/s12864-021-07636-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 04/21/2021] [Indexed: 11/17/2022] Open
Abstract
Background The complex life cycle of the coconut crab, Birgus latro, begins when an obligate terrestrial adult female visits the intertidal to hatch zoea larvae into the surf. After drifting for several weeks in the ocean, the post-larval glaucothoes settle in the shallow subtidal zone, undergo metamorphosis, and the early juveniles then subsequently make their way to land where they undergo further physiological changes that prevent them from ever entering the sea again. Here, we sequenced, assembled and analyzed the coconut crab genome to shed light on its adaptation to terrestrial life. For comparison, we also assembled the genomes of the long-tailed marine-living ornate spiny lobster, Panulirus ornatus, and the short-tailed marine-living red king crab, Paralithodes camtschaticus. Our selection of the latter two organisms furthermore allowed us to explore parallel evolution of the crab-like form in anomurans. Results All three assembled genomes are large, repeat-rich and AT-rich. Functional analysis reveals that the coconut crab has undergone proliferation of genes involved in the visual, respiratory, olfactory and cytoskeletal systems. Given that the coconut crab has atypical mitochondrial DNA compared to other anomurans, we argue that an abundance of kif22 and other significantly proliferated genes annotated with mitochondrial and microtubule functions, point to unique mechanisms involved in providing cellular energy via nuclear protein-coding genes supplementing mitochondrial and microtubule function. We furthermore detected in the coconut crab a significantly proliferated HOX gene, caudal, that has been associated with posterior development in Drosophila, but we could not definitively associate this gene with carcinization in the Anomura since it is also significantly proliferated in the ornate spiny lobster. However, a cuticle-associated coatomer gene, gammacop, that is significantly proliferated in the coconut crab, may play a role in hardening of the adult coconut crab abdomen in order to mitigate desiccation in terrestrial environments. Conclusion The abundance of genomic features in the three assembled genomes serve as a source of hypotheses for future studies of anomuran environmental adaptations such as shell-utilization, perception of visual and olfactory cues in terrestrial environments, and cuticle sclerotization. We hypothesize that the coconut crab exhibits gene proliferation in lieu of alternative splicing as a terrestrial adaptation mechanism and propose life-stage transcriptomic assays to test this hypothesis. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07636-9.
Collapse
Affiliation(s)
- Werner Pieter Veldsman
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.
| | - Ka Yan Ma
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Jerome Ho Lam Hui
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Ting Fung Chan
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - J Antonio Baeza
- Department of Biological Sciences, Clemson University, 132 Long Hall, Clemson, SC, 29634, USA.,Smithsonian Marine Station at Fort Pierce, 701 Seaway Drive, Fort Pierce, Florida, 34949, USA.,Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo, 1281, Coquimbo, Chile
| | - Jing Qin
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Ka Hou Chu
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.
| |
Collapse
|
34
|
Gao NL, He Z, Zhu Q, Jiang P, Hu S, Chen WH. Selection for Cheaper Amino Acids Drives Nucleotide Usage at the Start of Translation in Eukaryotic Genes. GENOMICS PROTEOMICS & BIOINFORMATICS 2021; 19:949-957. [PMID: 33741525 PMCID: PMC9403032 DOI: 10.1016/j.gpb.2021.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 05/30/2019] [Accepted: 08/18/2019] [Indexed: 12/04/2022]
Abstract
Coding regions have complex interactions among multiple selective forces, which are manifested as biases in nucleotide composition. Previous studies have revealed a decreasing GC gradient from the 5′-end to 3′-end of coding regions in various organisms. We confirmed that this gradient is universal in eukaryotic genes, but the decrease only starts from the ∼ 25th codon. This trend is mostly found in nonsynonymous (ns) sites at which the GC gradient is universal across the eukaryotic genome. Increased GC contents at ns sites result in cheaper amino acids, indicating a universal selection for energy efficiency toward the N-termini of encoded proteins. Within a genome, the decreasing GC gradient is intensified from lowly to highly expressed genes (more and more protein products), further supporting this hypothesis. This reveals a conserved selective constraint for cheaper amino acids at the translation start that drives the increased GC contents at ns sites. Elevated GC contents can facilitate transcription but result in a more stable local secondary structure around the start codon and subsequently impede translation initiation. Conversely, the GC gradients at four-fold and two-fold synonymous sites vary across species. They could decrease or increase, suggesting different constraints acting at the GC contents of different codon sites in different species. This study reveals that the overall GC contents at the translation start are consequences of complex interactions among several major biological processes that shape the nucleotide sequences, especially efficient energy usage.
Collapse
Affiliation(s)
- Na L Gao
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Institute for Computer Science and Cluster of Excellence on Plant Sciences, Heinrich Heine University, Duesseldorf 40225, Germany
| | - Zilong He
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China; State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Interdisciplinary Innovation Institute of Medicine and Engineering, Beihang University, Beijing 100191, China
| | - Qianhui Zhu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China; State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Puzi Jiang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Songnian Hu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China; State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Wei-Hua Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
| |
Collapse
|
35
|
Majda S, Beisser D, Boenigk J. Nutrient-driven genome evolution revealed by comparative genomics of chrysomonad flagellates. Commun Biol 2021; 4:328. [PMID: 33712682 PMCID: PMC7954800 DOI: 10.1038/s42003-021-01781-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 01/28/2021] [Indexed: 01/31/2023] Open
Abstract
Phototrophic eukaryotes have evolved mainly by the primary or secondary uptake of photosynthetic organisms. A return to heterotrophy occurred multiple times in various protistan groups such as Chrysophyceae, despite the expected advantage of autotrophy. It is assumed that the evolutionary shift to mixotrophy and further to heterotrophy is triggered by a differential importance of nutrient and carbon limitation. We sequenced the genomes of 16 chrysophyte strains and compared them in terms of size, function, and sequence characteristics in relation to photo-, mixo- and heterotrophic nutrition. All strains were sequenced with Illumina and partly with PacBio. Heterotrophic taxa have reduced genomes and a higher GC content of up to 59% as compared to phototrophic taxa. Heterotrophs have a large pan genome, but a small core genome, indicating a differential specialization of the distinct lineages. The pan genome of mixotrophs and heterotrophs taken together but not the pan genome of the mixotrophs alone covers the complete functionality of the phototrophic strains indicating a random reduction of genes. The observed ploidy ranges from di- to tetraploidy and was found to be independent of taxonomy or trophic mode. Our results substantiate an evolution driven by nutrient and carbon limitation.
Collapse
Affiliation(s)
- Stephan Majda
- Department of Biodiversity, University of Duisburg-Essen, Essen, Germany.
| | - Daniela Beisser
- Department of Biodiversity, University of Duisburg-Essen, Essen, Germany
| | - Jens Boenigk
- Department of Biodiversity, University of Duisburg-Essen, Essen, Germany
| |
Collapse
|
36
|
Ge Z, Li X, Cao X, Wang R, Hu W, Gen L, Han S, Shang Y, Liu Y, Zhou JH. Viral adaption of staphylococcal phage: A genome-based analysis of the selective preference based on codon usage Bias. Genomics 2020; 112:4657-4665. [PMID: 32818632 DOI: 10.1016/j.ygeno.2020.08.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 07/19/2020] [Accepted: 08/11/2020] [Indexed: 12/09/2022]
Abstract
Given the high therapeutic value of the staphylococcal phage, the genome co-evolution of the phage and the host has gained great attention. Though the genome-wide AT richness in staphylococcal phages has been well-studied with nucleotide usage bias, here we proved that host factor, lifestyle and taxonomy are also important factors in understanding the phage nucleotide usages bias using information entropy formula. Such correlation is especially prominent when it comes to the synonymous codon usages of staphylococcal phages, despite the overall scattered codon usage pattern represented by principal component analysis. This strong relationship is explained by nucleotide skew which testified that the usage biases of nucleotide at different codon positions are acting on synonymous codons. Therefore, our study reveals a hidden relationship of genome evolution with host limitation and phagic phenotype, providing new insight into phage genome evolution at genetic level.
Collapse
Affiliation(s)
- Zhiyi Ge
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, Gansu, PR China
| | - Xuerui Li
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, Gansu, PR China
| | - Xiaoan Cao
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, Gansu, PR China
| | - Rui Wang
- Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, United States of America
| | - Wen Hu
- Gansu Police Vocational College, Lanzhou 730046, Gansu, PR China
| | - Ling Gen
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, Gansu, PR China
| | - Shengyi Han
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, Gansu, PR China; The College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, Gansu Province, PR China
| | - Youjun Shang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, Gansu, PR China
| | - Yongsheng Liu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, Gansu, PR China
| | - Jian-Hua Zhou
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, Gansu, PR China.
| |
Collapse
|
37
|
Interplay between Position-Dependent Codon Usage Bias and Hydrogen Bonding at the 5' End of ORFeomes. mSystems 2020; 5:5/4/e00613-20. [PMID: 32788408 PMCID: PMC7426154 DOI: 10.1128/msystems.00613-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Codon usage bias exerts control over a wide variety of molecular processes. The positioning of synonymous codons within coding sequences (CDSs) dictates protein expression by mechanisms such as local translation efficiency, mRNA Gibbs free energy, and protein cotranslational folding. In this work, we explore how codon usage affects the position-dependent content of hydrogen bonding, which in turn influences energy requirements for unwinding double-stranded DNA (dsDNA). We categorized codons according to their hydrogen bond content and found differential effects on hydrogen bonding encoded by codon variants. The specific positional disposition of codon variants within CDSs creates a ramp of hydrogen bonding at the 5' end of the ORFeome in Escherichia coli CDSs occupying the first position of operons are subjected to selective pressure that reduces their hydrogen bonding compared to internal CDSs, and highly transcribed CDSs demand a lower maximum capacity of hydrogen bonds per codon, suggesting that the energetic requirement for unwinding the dsDNA in highly transcribed CDSs has evolved to be minimized in E. coli Subsequent analysis of over 14,000 ORFeomes showed a pervasive ramp of hydrogen bonding at the 5' end in Bacteria and Archaea that positively correlates with the probability of mRNA secondary structure formation. Both the ramp and the correlation were not found in Fungi The position-dependent hydrogen bonding might be part of the mechanism that contributes to the coordination between transcription and translation in Bacteria and Archaea A Web-based application to analyze the position-dependent hydrogen bonding of ORFeomes has been developed and is publicly available (https://juanvillada.shinyapps.io/hbonds/).IMPORTANCE Redundancy of the genetic code creates a vast space of alternatives to encode a protein. Synonymous codons exert control over a variety of molecular and physiological processes of cells mainly through influencing protein biosynthesis. Recent findings have shown that synonymous codon choice affects transcription by controlling mRNA abundance, mRNA stability, transcription termination, and transcript biosynthesis cost. In this work, by analyzing thousands of Bacteria, Archaea, and Fungi genomes, we extend recent findings by showing that synonymous codon choice, corresponding to the number of hydrogen bonds in a codon, can also have an effect on the energetic requirements for unwinding double-stranded DNA in a position-dependent fashion. This report offers new perspectives on the mechanism behind the transcription-translation coordination and complements previous hypotheses on the resource allocation strategies used by Bacteria and Archaea to manage energy efficiency in gene expression.
Collapse
|
38
|
Selection for Reducing Energy Cost of Protein Production Drives the GC Content and Amino Acid Composition Bias in Gene Transfer Agents. mBio 2020; 11:mBio.01206-20. [PMID: 32665274 PMCID: PMC7360931 DOI: 10.1128/mbio.01206-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Kin selection and group selection remain controversial topics in evolutionary biology. We argue that these types of selection are likely to operate in bacterial populations by showing that bacterial gene transfer agents (GTAs), but not related viruses, evolve under conditions of positive selection for the reduction of the energy cost of GTA particle production. We hypothesize that GTAs are dedicated devices mediating the survival of bacteria under conditions of nutrient limitation. The benefits conferred by GTAs under nutritional stress conditions appear to include horizontal dissemination of genes that could provide bacteria with enhanced capabilities for nutrient utilization and increases of nutrient availability occurring through the lysis of GTA-producing bacteria. Gene transfer agents (GTAs) are virus-like elements integrated into bacterial genomes, particularly, those of Alphaproteobacteria. The GTAs can be induced under conditions of nutritional stress, incorporate random fragments of bacterial DNA into miniphage particles, lyse the host cells, and infect neighboring bacteria, thus enhancing horizontal gene transfer. We show that GTA genes evolve under conditions of pronounced positive selection for the reduction of the energy cost of protein production as shown by comparison of the amino acid compositions with those of both homologous viral genes and host genes. The energy saving in GTA genes is comparable to or even more pronounced than that in the genes encoding the most abundant, essential bacterial proteins. In cases in which viruses acquire genes from GTAs, the bias in amino acid composition disappears in the course of evolution, showing that reduction of the energy cost of protein production is an important factor of evolution of GTAs but not bacterial viruses. These findings strongly suggest that GTAs represent bacterial adaptations rather than selfish, virus-like elements. Because GTA production kills the host cell and does not propagate the GTA genome, it appears likely that the GTAs are retained in the course of evolution via kin or group selection. Therefore, we hypothesize that GTAs facilitate the survival of bacterial populations under energy-limiting conditions through the spread of metabolic and transport capabilities via horizontal gene transfer and increases in nutrient availability resulting from the altruistic suicide of GTA-producing cells.
Collapse
|
39
|
Ohbayashi R, Hirooka S, Onuma R, Kanesaki Y, Hirose Y, Kobayashi Y, Fujiwara T, Furusawa C, Miyagishima SY. Evolutionary Changes in DnaA-Dependent Chromosomal Replication in Cyanobacteria. Front Microbiol 2020; 11:786. [PMID: 32411117 PMCID: PMC7198777 DOI: 10.3389/fmicb.2020.00786] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 04/02/2020] [Indexed: 12/02/2022] Open
Abstract
Replication of the circular bacterial chromosome is initiated at a unique origin (oriC) in a DnaA-dependent manner in which replication proceeds bidirectionally from oriC to ter. The nucleotide compositions of most bacteria differ between the leading and lagging DNA strands. Thus, the chromosomal DNA sequence typically exhibits an asymmetric GC skew profile. Further, free-living bacteria without genomes encoding dnaA were unknown. Thus, a DnaA-oriC-dependent replication initiation mechanism may be essential for most bacteria. However, most cyanobacterial genomes exhibit irregular GC skew profiles. We previously found that the Synechococcus elongatus chromosome, which exhibits a regular GC skew profile, is replicated in a DnaA-oriC-dependent manner, whereas chromosomes of Synechocystis sp. PCC 6803 and Nostoc sp. PCC 7120, which exhibit an irregular GC skew profile, are replicated from multiple origins in a DnaA-independent manner. Here we investigate the variation in the mechanisms of cyanobacterial chromosome replication. We found that the genomes of certain free-living species do not encode dnaA and such species, including Cyanobacterium aponinum PCC 10605 and Geminocystis sp. NIES-3708, replicate their chromosomes from multiple origins. Synechococcus sp. PCC 7002, which is phylogenetically closely related to dnaA-lacking free-living species as well as to dnaA-encoding but DnaA-oriC-independent Synechocystis sp. PCC 6803, possesses dnaA. In Synechococcus sp. PCC 7002, dnaA was not essential and its chromosomes were replicated from a unique origin in a DnaA-oriC independent manner. Our results also suggest that loss of DnaA-oriC-dependency independently occurred multiple times during cyanobacterial evolution and raises a possibility that the loss of dnaA or loss of DnaA-oriC dependency correlated with an increase in ploidy level.
Collapse
Affiliation(s)
- Ryudo Ohbayashi
- Department of Gene Function and Phenomics, National Institute of Genetics, Shizuoka, Japan
| | - Shunsuke Hirooka
- Department of Gene Function and Phenomics, National Institute of Genetics, Shizuoka, Japan
| | - Ryo Onuma
- Department of Gene Function and Phenomics, National Institute of Genetics, Shizuoka, Japan
| | - Yu Kanesaki
- Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Yuu Hirose
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi, Japan
| | - Yusuke Kobayashi
- Department of Gene Function and Phenomics, National Institute of Genetics, Shizuoka, Japan
| | - Takayuki Fujiwara
- Department of Gene Function and Phenomics, National Institute of Genetics, Shizuoka, Japan.,Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Shizuoka, Japan
| | - Chikara Furusawa
- Center for Biosystems Dynamics Research, RIKEN, Osaka, Japan.,Universal Biology Institute, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Shin-Ya Miyagishima
- Department of Gene Function and Phenomics, National Institute of Genetics, Shizuoka, Japan.,Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Shizuoka, Japan
| |
Collapse
|
40
|
Syeda AH, Dimude JU, Skovgaard O, Rudolph CJ. Too Much of a Good Thing: How Ectopic DNA Replication Affects Bacterial Replication Dynamics. Front Microbiol 2020; 11:534. [PMID: 32351461 PMCID: PMC7174701 DOI: 10.3389/fmicb.2020.00534] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 03/12/2020] [Indexed: 12/15/2022] Open
Abstract
Each cell division requires the complete and accurate duplication of the entire genome. In bacteria, the duplication process of the often-circular chromosomes is initiated at a single origin per chromosome, resulting in two replication forks that traverse the chromosome in opposite directions. DNA synthesis is completed once the two forks fuse in a region diametrically opposite the origin. In some bacteria, such as Escherichia coli, the region where forks fuse forms a specialized termination area. Polar replication fork pause sites flanking this area can pause the progression of replication forks, thereby allowing forks to enter but not to leave. Transcription of all required genes has to take place simultaneously with genome duplication. As both of these genome trafficking processes share the same template, conflicts are unavoidable. In this review, we focus on recent attempts to add additional origins into various ectopic chromosomal locations of the E. coli chromosome. As ectopic origins disturb the native replichore arrangements, the problems resulting from such perturbations can give important insights into how genome trafficking processes are coordinated and the problems that arise if this coordination is disturbed. The data from these studies highlight that head-on replication–transcription conflicts are indeed highly problematic and multiple repair pathways are required to restart replication forks arrested at obstacles. In addition, the existing data also demonstrate that the replication fork trap in E. coli imposes significant constraints to genome duplication if ectopic origins are active. We describe the current models of how replication fork fusion events can cause serious problems for genome duplication, as well as models of how such problems might be alleviated both by a number of repair pathways as well as the replication fork trap system. Considering the problems associated both with head-on replication-transcription conflicts as well as head-on replication fork fusion events might provide clues of how these genome trafficking issues have contributed to shape the distinct architecture of bacterial chromosomes.
Collapse
Affiliation(s)
- Aisha H Syeda
- Department of Biology, University of York, York, United Kingdom
| | - Juachi U Dimude
- Division of Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge, United Kingdom
| | - Ole Skovgaard
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Christian J Rudolph
- Division of Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge, United Kingdom
| |
Collapse
|
41
|
Zu H, Zhang H, Yao M, Zhang J, Di H, Zhang L, Dong L, Wang Z, Zhou Y. Molecular characteristics of segment 5, a unique fragment encoding two partially overlapping ORFs in the genome of rice black-streaked dwarf virus. PLoS One 2019; 14:e0224569. [PMID: 31697693 PMCID: PMC6837423 DOI: 10.1371/journal.pone.0224569] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 10/16/2019] [Indexed: 02/04/2023] Open
Abstract
Rice black-streaked dwarf virus (RBSDV), a ds-RNA virus in Fijivirus genus with family Reoviridae, which is transmitted by the small brown planthopper, is responsible for incidence of maize rough dwarf disease (MRDD) and rice black-streaked dwarf disease (RBSDD). To understand the variation and evolution of S5, a unique fragment in the genome of RBSDV which encodes two partially overlapping ORFs (ORF5-1 and ORF5-2), we analyzed 127 sequences from maize and rice exhibiting symptoms of dwarfism. The nucleotide diversity of both ORF5-1 (π = 0.039) and ORF5-2 (π = 0.027) was higher than that of the overlapping region (π = 0.011) (P < 0.05). ORF5-2 was under the greatest selection pressure based on codon bias analysis, and its activation was possibly influenced by the overlapping region. The recombinant fragments of three recombinant events (14NM23, 14BM20, and 14NM17) cross the overlapping region. Based on neighbor-joining tree analysis, the overlapping region could represent the evolutionary basis of the full-length S5, which was classified into three main groups. RBSDV populations were expanding and haplotype diversity resulted mainly from the overlapping region. The genetic differentiation of combinations (T127-B35, T127-J34, A58-B35, A58-J34, and B35-J34) reached significant or extremely significant levels. Gene flow was most frequent between subpopulations A58 and B35, with the smallest |Fst| (0.02930). We investigated interactions between 13 RBSDV proteins by two-hybrid screening assays and identified interactions between P5-1/P6, P6/P9-1, and P3/P6. We also observed self-interactive effects of P3, P6, P7-1, and P10. In short, we have proven that RBSDV populations were expanding and the overlapping region plays an important role in the genetic variation and evolution of RBSDV S5. Our results enable ongoing research into the evolutionary history of RBSDV-S5 with two partly overlapping ORFs.
Collapse
Affiliation(s)
- Hongyue Zu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Northeast Agricultural University, Changjiang Road, Xiangfang District, Harbin, Heilongjiang Province, China
| | - Hong Zhang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Northeast Agricultural University, Changjiang Road, Xiangfang District, Harbin, Heilongjiang Province, China
| | - Minhao Yao
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Northeast Agricultural University, Changjiang Road, Xiangfang District, Harbin, Heilongjiang Province, China
| | - Jiayue Zhang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Northeast Agricultural University, Changjiang Road, Xiangfang District, Harbin, Heilongjiang Province, China
| | - Hong Di
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Northeast Agricultural University, Changjiang Road, Xiangfang District, Harbin, Heilongjiang Province, China
| | - Lin Zhang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Northeast Agricultural University, Changjiang Road, Xiangfang District, Harbin, Heilongjiang Province, China
| | - Ling Dong
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Northeast Agricultural University, Changjiang Road, Xiangfang District, Harbin, Heilongjiang Province, China
| | - Zhenhua Wang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Northeast Agricultural University, Changjiang Road, Xiangfang District, Harbin, Heilongjiang Province, China
- * E-mail: (YZ); (ZHW)
| | - Yu Zhou
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Northeast Agricultural University, Changjiang Road, Xiangfang District, Harbin, Heilongjiang Province, China
- * E-mail: (YZ); (ZHW)
| |
Collapse
|
42
|
Gao NL, Chen J, Wang T, Lercher MJ, Chen WH. Prokaryotic Genome Expansion Is Facilitated by Phages and Plasmids but Impaired by CRISPR. Front Microbiol 2019; 10:2254. [PMID: 31681190 PMCID: PMC6805729 DOI: 10.3389/fmicb.2019.02254] [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: 04/28/2019] [Accepted: 09/17/2019] [Indexed: 12/02/2022] Open
Abstract
Viruses and plasmids can introduce novel DNA into bacterial cells, thereby creating an opportunity for genome expansion; conversely, CRISPR, the prokaryotic adaptive immune system, which targets and eliminates foreign DNAs, may impair genome expansions. Recent studies presented conflicting results over the impact of CRISPR on genome expansion. In this study, we constructed a comprehensive dataset of prokaryotic genomes and identified their associations with viruses and plasmids. We found that genomes associated with viruses and/or plasmids were significantly larger than those without, indicating that both viruses and plasmids contribute to genome expansion. Genomes were increasingly larger with increasing numbers of associated viruses or plasmids. Conversely, genomes with CRISPR systems were significantly smaller than those without, indicating that CRISPR has a negative impact on genome size. These results confirmed that on evolutionary timescales, viruses and plasmids facilitate genome expansion, while CRISPR impairs such a process in prokaryotes. Furthermore, our results also revealed that CRISPR systems show a preference for targeting viruses over plasmids.
Collapse
Affiliation(s)
- Na L Gao
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.,Institute for Computer Science and Department of Biology, Heinrich Heine University, Duesseldorf, Germany
| | - Jingchao Chen
- College of Life Science, Henan Normal University, Xinxiang, China
| | - Teng Wang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Martin J Lercher
- Institute for Computer Science and Department of Biology, Heinrich Heine University, Duesseldorf, Germany
| | - Wei-Hua Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.,College of Life Science, Henan Normal University, Xinxiang, China.,Huazhong University of Science and Technology Ezhou Industrial Technology Research Institute, Ezhou, China
| |
Collapse
|
43
|
Affiliation(s)
- Itai Yanai
- Institute for Computational Medicine, NYU Langone Health, New York, NY, 10016, USA.
| | - Martin Lercher
- Institute for Computer Science & Department of Biology, Heinrich Heine University, 40225, Düsseldorf, Germany.
| |
Collapse
|
44
|
Mordret E, Dahan O, Asraf O, Rak R, Yehonadav A, Barnabas GD, Cox J, Geiger T, Lindner AB, Pilpel Y. Systematic Detection of Amino Acid Substitutions in Proteomes Reveals Mechanistic Basis of Ribosome Errors and Selection for Translation Fidelity. Mol Cell 2019; 75:427-441.e5. [DOI: 10.1016/j.molcel.2019.06.041] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 03/05/2019] [Accepted: 06/26/2019] [Indexed: 11/26/2022]
|
45
|
Genomic Evidence for Simultaneous Optimization of Transcription and Translation through Codon Variants in the pmoCAB Operon of Type Ia Methanotrophs. mSystems 2019; 4:4/4/e00342-19. [PMID: 31337658 PMCID: PMC6650546 DOI: 10.1128/msystems.00342-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Microbial methane oxidation plays a fundamental role in the biogeochemical cycle of Earth’s system. Recent reports have provided evidence for the acquisition of methane monooxygenases by horizontal gene transfer in methane-oxidizing bacteria from different environments, but how evolution has shaped the coding sequences to execute methanotrophy efficiently remains unexplored. In this work, we provide genomic evidence that among the different types of methanotrophs, type Ia methanotrophs possess a unique coding sequence of the pmoCAB operon that is under positive selection for optimal resource allocation and efficient synthesis of transcripts and proteins. This adaptive trait possibly enables type Ia methanotrophs to respond robustly to fluctuating methane availability and explains their global prevalence. Understanding the interplay between genotype and phenotype is a fundamental goal of functional genomics. Methane oxidation is a microbial phenotype with global-scale significance as part of the carbon biogeochemical cycle and a sink for greenhouse gas. Microorganisms that oxidize methane (methanotrophs) are taxonomically diverse and widespread around the globe. In methanotrophic bacteria, enzymes in the methane oxidation metabolic module (KEGG module M00174, conversion of methane to formaldehyde) are encoded in four operons (pmoCAB, mmoXYZBCD, mxaFI, and xoxF). Recent reports have suggested that methanotrophs in Proteobacteria acquired methane monooxygenases through horizontal gene transfer. Here, we used a genomic meta-analysis to infer the transcriptional and translational advantages of coding sequences from the methane oxidation metabolic modules of different types of methanotrophs. By analyzing isolate and metagenome-assembled genomes from phylogenetically and geographically diverse sources, we detected an anomalous nucleotide composition bias in the coding sequences of particulate methane monooxygenase genes (pmoCAB) from type Ia methanotrophs. We found that this nucleotide bias increases the level of codon bias by decreasing the GC content in the third base of codons, a strategy that contrasts with that of other coding sequences in the module. Further codon usage analyses uncovered that codon variants of the type Ia pmoCAB coding sequences deviate from the genomic signature to match ribosomal protein-coding sequences. Subsequently, computation of transcription and translation metrics revealed that the pmoCAB coding sequences of type Ia methanotrophs optimize the usage of codon variants to maximize translation efficiency and accuracy, while minimizing the synthesis cost of transcripts and proteins. IMPORTANCE Microbial methane oxidation plays a fundamental role in the biogeochemical cycle of Earth’s system. Recent reports have provided evidence for the acquisition of methane monooxygenases by horizontal gene transfer in methane-oxidizing bacteria from different environments, but how evolution has shaped the coding sequences to execute methanotrophy efficiently remains unexplored. In this work, we provide genomic evidence that among the different types of methanotrophs, type Ia methanotrophs possess a unique coding sequence of the pmoCAB operon that is under positive selection for optimal resource allocation and efficient synthesis of transcripts and proteins. This adaptive trait possibly enables type Ia methanotrophs to respond robustly to fluctuating methane availability and explains their global prevalence.
Collapse
|
46
|
Wang J, Li X, Do Kim K, Scanlon MJ, Jackson SA, Springer NM, Yu J. Genome-wide nucleotide patterns and potential mechanisms of genome divergence following domestication in maize and soybean. Genome Biol 2019; 20:74. [PMID: 31018867 PMCID: PMC6482504 DOI: 10.1186/s13059-019-1683-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 03/28/2019] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Plant domestication provides a unique model to study genome evolution. Many studies have been conducted to examine genes, genetic diversity, genome structure, and epigenome changes associated with domestication. Interestingly, domesticated accessions have significantly higher [A] and [T] values across genome-wide polymorphic sites than accessions sampled from the corresponding progenitor species. However, the relative contributions of different genomic regions to this genome divergence pattern and underlying mechanisms have not been well characterized. RESULTS Here, we investigate the genome-wide base-composition patterns by analyzing millions of SNPs segregating among 100 accessions from a teosinte-maize comparison set and among 302 accessions from a wild-domesticated soybean comparison set. We show that non-genic part of the genome has a greater contribution than genic SNPs to the [AT]-increase observed between wild and domesticated accessions in maize and soybean. The separation between wild and domesticated accessions in [AT] values is significantly enlarged in non-genic and pericentromeric regions. Motif frequency and sequence context analyses show the motifs (PyCG) related to solar-UV signature are enriched in these regions, particularly when they are methylated. Additional analysis using population-private SNPs also implicates the role of these motifs in relatively recent mutations. With base-composition across polymorphic sites as a genome phenotype, genome scans identify a set of putative candidate genes involved in UV damage repair pathways. CONCLUSIONS The [AT]-increase is more pronounced in genomic regions that are non-genic, pericentromeric, transposable elements; methylated; and with low recombination. Our findings establish important links among UV radiation, mutation, DNA repair, methylation, and genome evolution.
Collapse
Affiliation(s)
- Jinyu Wang
- Department of Agronomy, Iowa State University, Ames, IA 50011 USA
| | - Xianran Li
- Department of Agronomy, Iowa State University, Ames, IA 50011 USA
| | - Kyung Do Kim
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602 USA
| | - Michael J. Scanlon
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853 USA
| | - Scott A. Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602 USA
| | - Nathan M. Springer
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108 USA
| | - Jianming Yu
- Department of Agronomy, Iowa State University, Ames, IA 50011 USA
| |
Collapse
|
47
|
Bohlin J, Pettersson JHO. Evolution of Genomic Base Composition: From Single Cell Microbes to Multicellular Animals. Comput Struct Biotechnol J 2019; 17:362-370. [PMID: 30949307 PMCID: PMC6429543 DOI: 10.1016/j.csbj.2019.03.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 02/28/2019] [Accepted: 03/01/2019] [Indexed: 01/07/2023] Open
Abstract
Whole genome sequencing (WGS) of thousands of microbial genomes has provided considerable insight into evolutionary mechanisms in the microbial world. While substantially fewer eukaryotic genomes are available for analyses the number is rapidly increasing. This mini-review summarizes broadly evolutionary dynamics of base composition in the different domains of life from the perspective of prokaryotes. Common and different evolutionary mechanisms influencing genomic base composition in eukaryotes and prokaryotes are discussed. The conclusion from the data currently available suggests that while there are similarities there are also striking differences in how genomic base composition has evolved within prokaryotes and eukaryotes. For instance, homologous recombination appears to increase GC content locally in eukaryotes due to a non-selective process termed GC-biased gene conversion (gBGC). For prokaryotes on the other hand, increase in genomic GC content seems to be driven by the environment and selection. We find that similar phenomena observed for some organisms in each respective domain may be caused by very different mechanisms: while gBGC and recombination rates appear to explain the negative correlation between GC3 (GC content based on the third codon nucleotides) and genome size in some eukaryotes uptake of AT rich DNA sequences is the main reason for a similar negative correlation observed in prokaryotes. We provide further examples that indicate that base composition in prokaryotes and eukaryotes have evolved under very different constraints.
Collapse
Affiliation(s)
- Jon Bohlin
- Norwegian Institute of Public Health, Division of Infection Control and Environmental Health, Department of Infectious Disease Epidemiology and Modelling, Lovisenberggata 8, 0456 Oslo, Norway.,Centre for Fertility and Health, Norwegian Institute of Public Health, PO-Box 222 Skøyen, N-0213 Oslo, Norway.,Norwegian University of Life Sciences, Faculty of Veterinary Sciences, Production Animal Clinical Sciences, Ullevålsveien 72, 0454 Oslo, Norway
| | - John H-O Pettersson
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School the University of Sydney, New South Wales 2006, Australia.,Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.,Public Health Agency of Sweden, Nobels vg 18, SE-171 82 Solna, Sweden
| |
Collapse
|
48
|
Su HJ, Barkman TJ, Hao W, Jones SS, Naumann J, Skippington E, Wafula EK, Hu JM, Palmer JD, dePamphilis CW. Novel genetic code and record-setting AT-richness in the highly reduced plastid genome of the holoparasitic plant Balanophora. Proc Natl Acad Sci U S A 2019; 116:934-943. [PMID: 30598433 PMCID: PMC6338844 DOI: 10.1073/pnas.1816822116] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Plastid genomes (plastomes) vary enormously in size and gene content among the many lineages of nonphotosynthetic plants, but key lineages remain unexplored. We therefore investigated plastome sequence and expression in the holoparasitic and morphologically bizarre Balanophoraceae. The two Balanophora plastomes examined are remarkable, exhibiting features rarely if ever seen before in plastomes or in any other genomes. At 15.5 kb in size and with only 19 genes, they are among the most reduced plastomes known. They have no tRNA genes for protein synthesis, a trait found in only three other plastid lineages, and thus Balanophora plastids must import all tRNAs needed for translation. Balanophora plastomes are exceptionally compact, with numerous overlapping genes, highly reduced spacers, loss of all cis-spliced introns, and shrunken protein genes. With A+T contents of 87.8% and 88.4%, the Balanophora genomes are the most AT-rich genomes known save for a single mitochondrial genome that is merely bloated with AT-rich spacer DNA. Most plastid protein genes in Balanophora consist of ≥90% AT, with several between 95% and 98% AT, resulting in the most biased codon usage in any genome described to date. A potential consequence of its radical compositional evolution is the novel genetic code used by Balanophora plastids, in which TAG has been reassigned from stop to tryptophan. Despite its many exceptional properties, the Balanophora plastome must be functional because all examined genes are transcribed, its only intron is correctly trans-spliced, and its protein genes, although highly divergent, are evolving under various degrees of selective constraint.
Collapse
Affiliation(s)
- Huei-Jiun Su
- Department of Earth and Life Sciences, University of Taipei, 100 Taipei, Taiwan
- Department of Biology, Pennsylvania State University, University Park, PA 16802
- Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park, PA 16802
| | - Todd J Barkman
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Weilong Hao
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202
| | - Samuel S Jones
- Graduate Program in Plant Biology, Pennsylvania State University, University Park, PA 16802
| | - Julia Naumann
- Department of Biology, Pennsylvania State University, University Park, PA 16802
- Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park, PA 16802
| | | | - Eric K Wafula
- Department of Biology, Pennsylvania State University, University Park, PA 16802
- Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park, PA 16802
| | - Jer-Ming Hu
- Institute of Ecology and Evolutionary Biology, National Taiwan University, 106 Taipei, Taiwan
| | - Jeffrey D Palmer
- Department of Biology, Indiana University, Bloomington, IN 47405;
| | - Claude W dePamphilis
- Department of Biology, Pennsylvania State University, University Park, PA 16802;
- Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park, PA 16802
- Graduate Program in Plant Biology, Pennsylvania State University, University Park, PA 16802
| |
Collapse
|
49
|
Synonymous Codon Usages as an Evolutionary Dynamic for Chlamydiaceae. Int J Mol Sci 2018; 19:ijms19124010. [PMID: 30545112 PMCID: PMC6321445 DOI: 10.3390/ijms19124010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 12/06/2018] [Accepted: 12/10/2018] [Indexed: 01/08/2023] Open
Abstract
The family of Chlamydiaceae contains a group of obligate intracellular bacteria that can infect a wide range of hosts. The evolutionary trend of members in this family is a hot topic, which benefits our understanding of the cross-infection of these pathogens. In this study, 14 whole genomes of 12 Chlamydia species were used to investigate the nucleotide, codon, and amino acid usage bias by synonymous codon usage value and information entropy method. The results showed that all the studied Chlamydia spp. had A/T rich genes with over-represented A or T at the third positions and G or C under-represented at these positions, suggesting that nucleotide usages influenced synonymous codon usages. The overall codon usage trend from synonymous codon usage variations divides the Chlamydia spp. into four separate clusters, while amino acid usage divides the Chlamydia spp. into two clusters with some exceptions, which reflected the genetic diversity of the Chlamydiaceae family members. The overall codon usage pattern represented by the effective number of codons (ENC) was significantly positively correlated to gene GC3 content. A negative correlation exists between ENC and the codon adaptation index for some Chlamydia species. These results suggested that mutation pressure caused by nucleotide composition constraint played an important role in shaping synonymous codon usage patterns. Furthermore, codon usage of T3ss and Pmps gene families adapted to that of the corresponding genome. Taken together, analyses help our understanding of evolutionary interactions between nucleotide, synonymous codon, and amino acid usages in genes of Chlamydiaceae family members.
Collapse
|
50
|
Du MZ, Zhang C, Wang H, Liu S, Wei W, Guo FB. The GC Content as a Main Factor Shaping the Amino Acid Usage During Bacterial Evolution Process. Front Microbiol 2018; 9:2948. [PMID: 30581420 PMCID: PMC6292993 DOI: 10.3389/fmicb.2018.02948] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 11/16/2018] [Indexed: 11/13/2022] Open
Abstract
Understanding how proteins evolve is important, and the order of amino acids being recruited into the genetic codons was found to be an important factor shaping the amino acid composition of proteins. The latest work about the last universal common ancestor (LUCA) makes it possible to determine the potential factors shaping amino acid compositions during evolution. Those LUCA genes/proteins from Methanococcus maripaludis S2, which is one of the possible LUCA, were investigated. The evolutionary rates of these genes positively correlate with GC contents with P-value significantly lower than 0.05 for 94% homologous genes. Linear regression results showed that compositions of amino acids coded by GC-rich codons positively contribute to the evolutionary rates, while these amino acids tend to be gained in GC-rich organisms according to our results. The first principal component correlates with the GC content very well. The ratios of amino acids of the LUCA proteins coded by GC rich codons positively correlate with the GC content of different bacteria genomes, while the ratios of amino acids coded by AT rich codons negatively correlate with the increase of GC content of genomes. Next, we found that the recruitment order does correlate with the amino acid compositions, but gain and loss in codons showed newly recruited amino acids are not significantly increased along with the evolution. Thus, we conclude that GC content is a primary factor shaping amino acid compositions. GC content shapes amino acid composition to trade off the cost of amino acids with bases, which could be caused by the energy efficiency.
Collapse
Affiliation(s)
- Meng-Ze Du
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | | | - Huan Wang
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Shuo Liu
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Wen Wei
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Feng-Biao Guo
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
- Centre for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| |
Collapse
|