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] [MESH Headings] [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
|
Chen H, Chen Y, Wang Z, Wu D, Chen P, Chen Y. The Complete Mitochondrial Genome of the Siberian Scoter Melanitta stejnegeri and Its Phylogenetic Relationship in Anseriformes. Int J Mol Sci 2024; 25:10181. [PMID: 39337666 PMCID: PMC11432269 DOI: 10.3390/ijms251810181] [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: 08/26/2024] [Revised: 09/19/2024] [Accepted: 09/20/2024] [Indexed: 09/30/2024] Open
Abstract
The Siberian Scoter (Melanitta stejnegeri) is a medium sea duck distinct from M. deglandi due to the absence of hybridization and differences in morphological characteristics. However, knowledge of its phylogenetic relationships within Anseriformes is limited due to a lack of molecular data. In this study, the complete mitogenome of M. stejnegeri was firstly sequenced, then annotated and used to reconstruct the phylogenetic relationships of 76 Anseriformes species. The complete mitogenome of M. stejnegeri is 16,631 bp and encodes 37 typical genes: 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and 1 non-coding control region. Its mitogenome organization is similar to that of other Anseriformes species. The phylogenetic relationships within the genus Melanitta are initially clarified, with M. americana at the base. M. stejnegeri and M. deglandi are sister groups, clustering with M. fusca and M. perspicillata in order. Phylogenetic analysis suggests that Mareca falcata and M. strepera are sister groups, differing from previous studies. Results firstly indicate that Clangula hyemalis and Somateria mollissima are sister groups, suggesting a potentially skewed phylogenetic relationship may have been overlooked in earlier analyses relying solely on mitochondrial genomes. Our results provide new mitogenome data to support further phylogenetic and taxonomic studies of Anseriformes.
Collapse
Affiliation(s)
- Huimin Chen
- The Anhui Provincial Key Laboratory of Biodiversity Conservation and Ecological Security in the Yangtze River Basin, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Yaqin Chen
- The Anhui Provincial Key Laboratory of Biodiversity Conservation and Ecological Security in the Yangtze River Basin, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Zhenqi Wang
- College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Dawei Wu
- College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Pan Chen
- The Anhui Provincial Key Laboratory of Biodiversity Conservation and Ecological Security in the Yangtze River Basin, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Yanhong Chen
- The Anhui Provincial Key Laboratory of Biodiversity Conservation and Ecological Security in the Yangtze River Basin, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| |
Collapse
|
3
|
Xu T, Xu W, Zhang G, Liu Z, Liu H. Characterization of the complete mitochondrial genomes of four tarantulas (Arachnida: Theraphosidae) with phylogenetic analysis. Gene 2024; 933:148954. [PMID: 39303821 DOI: 10.1016/j.gene.2024.148954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2024] [Revised: 09/03/2024] [Accepted: 09/17/2024] [Indexed: 09/22/2024]
Abstract
To better understand the evolution of mitochondrial genomes (mitogenomes) within the family Theraphosidae, we characterized mitogenomes of four tarantulas (Grammostola pulchripes, Phormictopus atrichomatus, Pterinochilus murinus and Pterinopelma sazimai) for the first time. The mitogenomes were all classical circular structures, with lengths ranging from 13,822 bp to 14,011 bp. The constitutive genes and the orientation of the coding strand observed in the four mitogenomes were consistent with those found in other species belonging to the Theraphosidae family. The four mitogenomes were compacted and exhibited a preference for A and T, with the rRNA sequences showing a higher A+T content. Ka/Ks and p-distances analyses showed the ND6 gene had highest evolutionary rate, while the COⅠ gene displayed relatively slower evolution. In contrast to previous phylogenetic studies, our phylogenetic analysis based on mitogenomes provides new phylogenetic relationships among subfamilies. Subfamily Theraphosinae is most closely related to Ornithoctoninae, slightly distant from Harpactirinae, and farthest from Selenocosmiinae. The new data we acquired regarding these mitogenomes will aid in understanding the complex interrelationships among species within the Theraphosidae family.
Collapse
Affiliation(s)
- Tangjun Xu
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Wei Xu
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Gaoji Zhang
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Zeyang Liu
- School of Mechanical and Electronic Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Hongyi Liu
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China.
| |
Collapse
|
4
|
Liu Q, Xu S, He J, Cai W, Wang X, Song F. Full-Length Transcriptome Profiling of the Complete Mitochondrial Genome of Sericothrips houjii (Thysanoptera: Thripidae: Sericothripinae) Featuring Extensive Gene Rearrangement and Duplicated Control Regions. INSECTS 2024; 15:700. [PMID: 39336667 PMCID: PMC11432214 DOI: 10.3390/insects15090700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2024] [Revised: 09/06/2024] [Accepted: 09/12/2024] [Indexed: 09/30/2024]
Abstract
The mitochondrial genome (mitogenome) of Thysanoptera has extensive gene rearrangement, and some species have repeatable control regions. To investigate the characteristics of the gene expression, transcription and post-transcriptional processes in such extensively gene-rearranged mitogenomes, we sequenced the mitogenome and mitochondrial transcriptome of Sericothrips houjii to analyze. The mitogenome was 14,965 bp in length and included two CRs contains 140 bp repeats between COIII-trnN (CR1) and trnT-trnP (CR2). Unlike the putative ancestral arrangement of insects, S. houjii exhibited only six conserved gene blocks encompassing 14 genes (trnL2-COII, trnD-trnK, ND2-trnW, ATP8-ATP6, ND5-trnH-ND4-ND4L and trnV-lrRNA). A quantitative transcription map showed the gene with the highest relative expression in the mitogenome was ND4-ND4L. Based on analyses of polycistronic transcripts, non-coding RNAs (ncRNAs) and antisense transcripts, we proposed a transcriptional model of this mitogenome. Both CRs contained the transcription initiation sites (TISs) and transcription termination sites (TTSs) of both strands, and an additional TIS for the majority strand (J-strand) was found within antisense lrRNA. The post-transcriptional cleavage processes followed the "tRNA punctuation" model. After the cleavage of transfer RNAs (tRNAs), COI and ND3 matured as bicistronic mRNA COI/ND3 due to the translocation of intervening tRNAs, and the 3' untranslated region (UTR) remained in the mRNAs for COII, COIII, CYTB and ND5. Additionally, isoform RNAs of ND2, srRNA and lrRNA were identified. In summary, the relative mitochondrial gene expression levels, transcriptional model and post-transcriptional cleavage process of S. houjii are notably different from those insects with typical mitochondrial gene arrangements. In addition, the phylogenetic tree of Thripidae including S. houjii was reconstructed. Our study provides insights into the phylogenetic status of Sericothripinae and the transcriptional and post-transcriptional regulation processes of extensively gene-rearranged insect mitogenomes.
Collapse
Affiliation(s)
- Qiaoqiao Liu
- Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou 510640, China
- MOA Key Lab of Pest Monitoring and Green Management, Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Shiwen Xu
- MOA Key Lab of Pest Monitoring and Green Management, Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Jia He
- MOA Key Lab of Pest Monitoring and Green Management, Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China
- Ningxia Key Lab of Plant Disease and Pest Control, Institute of Plant Protection, Ningxia Academy of Agriculture and Forestry Science, Yinchuan 750002, China
| | - Wanzhi Cai
- MOA Key Lab of Pest Monitoring and Green Management, Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Xingmin Wang
- Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou 510640, China
| | - Fan Song
- MOA Key Lab of Pest Monitoring and Green Management, Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| |
Collapse
|
5
|
Klirs Y, Novosolov M, Gissi C, Garić R, Pupko T, Stach T, Huchon D. Evolutionary Insights from the Mitochondrial Genome of Oikopleura dioica: Sequencing Challenges, RNA Editing, Gene Transfers to the Nucleus, and tRNA Loss. Genome Biol Evol 2024; 16:evae181. [PMID: 39162337 PMCID: PMC11384887 DOI: 10.1093/gbe/evae181] [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: 05/04/2024] [Revised: 07/19/2024] [Accepted: 08/13/2024] [Indexed: 08/21/2024] Open
Abstract
Sequencing the mitochondrial genome of the tunicate Oikopleura dioica is a challenging task due to the presence of long poly-A/T homopolymer stretches, which impair sequencing and assembly. Here, we report on the sequencing and annotation of the majority of the mitochondrial genome of O. dioica by means of combining several DNA and amplicon reads obtained by Illumina and MinIon Oxford Nanopore Technologies with public RNA sequences. We document extensive RNA editing, since all homopolymer stretches present in the mitochondrial DNA correspond to 6U-regions in the mitochondrial RNA. Out of the 13 canonical protein-coding genes, we were able to detect eight, plus an unassigned open reading frame that lacked sequence similarity to canonical mitochondrial protein-coding genes. We show that the nad3 gene has been transferred to the nucleus and acquired a mitochondria-targeting signal. In addition to two very short rRNAs, we could only identify a single tRNA (tRNA-Met), suggesting multiple losses of tRNA genes, supported by a corresponding loss of mitochondrial aminoacyl-tRNA synthetases in the nuclear genome. Based on the eight canonical protein-coding genes identified, we reconstructed maximum likelihood and Bayesian phylogenetic trees and inferred an extreme evolutionary rate of this mitochondrial genome. The phylogenetic position of appendicularians among tunicates, however, could not be accurately determined.
Collapse
Affiliation(s)
- Yael Klirs
- George S. Wise Faculty of Life Sciences, School of Zoology, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Maria Novosolov
- George S. Wise Faculty of Life Sciences, School of Zoology, Tel Aviv University, Tel Aviv 6997801, Israel
- Faculty of Health and Medical Sciences, GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Carmela Gissi
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Bari 70126, Italy
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, Bari 70126, Italy
- CoNISMa, Consorzio Nazionale Interuniversitario per le Scienze del Mare, Roma 00196, Italy
| | - Rade Garić
- Institute for Marine and Coastal Research, University of Dubrovnik, Dubrovnik 20000, Croatia
| | - Tal Pupko
- George S. Wise Faculty of Life Sciences, The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Thomas Stach
- Department of Molecular Parasitology, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Dorothée Huchon
- George S. Wise Faculty of Life Sciences, School of Zoology, Tel Aviv University, Tel Aviv 6997801, Israel
- The Steinhardt Museum of Natural History and National Research Center, Tel Aviv University, Tel Aviv 6997801, Israel
| |
Collapse
|
6
|
Zheng X, Lin X, Zhang X, Huang X, Yue X, Pu J. Complete mitochondrial genome of Penicillidia dufourii (Diptera: Hippoboscoidea: Nycteribiidae) and phylogenetic relationship. Parasitol Res 2024; 123:302. [PMID: 39158739 DOI: 10.1007/s00436-024-08321-y] [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: 05/31/2024] [Accepted: 08/08/2024] [Indexed: 08/20/2024]
Abstract
Penicillidia dufourii (Westwood 1834) is a specialized parasite categorized under family Nycteribiidae that prefers to parasitize the body surface of various bats under the genus Myotis. Many species of the family Nycteribiidae are carriers of various pathogens; however, research on P. dufourii remains scarce, and studies on its molecular identification and population genetic structure are still lacking. In this study, the complete mitochondrial genome of P. dufourii was elucidated for the first time using Illumina sequencing. The mitochondrial genome is 15,354 bp in size and encodes approximately 37 genes, including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 control region. Analysis of 13 protein-coding genes revealed that UUA, UCA, CGA, and GGA were the most common codons, while nad4L had the fastest evolutionary rate and cox1 the slowest. Phylogenetic analysis based on the mitochondrial genome indicated that P. dufourii is clustered with other species of the family Nycteribiidae and is most closely related to Nycteribia parvula and Phthiridium szechuanum.
Collapse
Affiliation(s)
- Xiaoyan Zheng
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Institute of Pathogens and Vectors, Dali University, Dali, 671000, Yunnan, China
| | - Xiaoxia Lin
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Institute of Pathogens and Vectors, Dali University, Dali, 671000, Yunnan, China
| | - Xianzheng Zhang
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Institute of Pathogens and Vectors, Dali University, Dali, 671000, Yunnan, China
| | - Xiaobin Huang
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Institute of Pathogens and Vectors, Dali University, Dali, 671000, Yunnan, China.
| | - Xinke Yue
- School of Life Sciences, Yunnan Normal University, Kunming, 650000, China.
| | - Ju Pu
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Institute of Pathogens and Vectors, Dali University, Dali, 671000, Yunnan, China
| |
Collapse
|
7
|
Kim S, Tan S, Ku J, Widowati TA, Ku D, Lee K, You K, Kim Y. RNA 5-methylcytosine marks mitochondrial double-stranded RNAs for degradation and cytosolic release. Mol Cell 2024; 84:2935-2948.e7. [PMID: 39019044 PMCID: PMC11316625 DOI: 10.1016/j.molcel.2024.06.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 05/20/2024] [Accepted: 06/21/2024] [Indexed: 07/19/2024]
Abstract
Mitochondria are essential regulators of innate immunity. They generate long mitochondrial double-stranded RNAs (mt-dsRNAs) and release them into the cytosol to trigger an immune response under pathological stress conditions. Yet the regulation of these self-immunogenic RNAs remains largely unknown. Here, we employ CRISPR screening on mitochondrial RNA (mtRNA)-binding proteins and identify NOP2/Sun RNA methyltransferase 4 (NSUN4) as a key regulator of mt-dsRNA expression in human cells. We find that NSUN4 induces 5-methylcytosine (m5C) modification on mtRNAs, especially on the termini of light-strand long noncoding RNAs. These m5C-modified RNAs are recognized by complement C1q-binding protein (C1QBP), which recruits polyribonucleotide nucleotidyltransferase to facilitate RNA turnover. Suppression of NSUN4 or C1QBP results in increased mt-dsRNA expression, while C1QBP deficiency also leads to increased cytosolic mt-dsRNAs and subsequent immune activation. Collectively, our study unveils the mechanism underlying the selective degradation of light-strand mtRNAs and establishes a molecular mark for mtRNA decay and cytosolic release.
Collapse
Affiliation(s)
- Sujin Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Stephanie Tan
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Jayoung Ku
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Tria Asri Widowati
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Doyeong Ku
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Keonyong Lee
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Kwontae You
- Xaira Therapeutics, Foster City, CA 94404, USA
| | - Yoosik Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; Graduate School of Engineering Biology, KAIST, Daejeon 34141, Republic of Korea; KAIST Institute for BioCentury, KAIST, Daejeon 34141, Republic of Korea; KAIST Institute for Health Science and Technology (KIHST), KAIST, Daejeon 34141, Republic of Korea.
| |
Collapse
|
8
|
Bukina V, Božič A. Context-dependent structure formation of hairpin motifs in bacteriophage MS2 genomic RNA. Biophys J 2024:S0006-3495(24)00526-5. [PMID: 39118324 DOI: 10.1016/j.bpj.2024.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 07/17/2024] [Accepted: 08/05/2024] [Indexed: 08/10/2024] Open
Abstract
Many functions of ribonucleic acid (RNA) rely on its ability to assume specific sequence-structure motifs. Packaging signals found in certain RNA viruses are one such prominent example of functional RNA motifs. These signals are short hairpin loops that interact with coat proteins and drive viral self-assembly. As they are found in different positions along the much longer genomic RNA, the formation of their correct structure occurs as a part of a larger context. Any changes to this context can consequently lead to changes in the structure of the motifs themselves. In fact, previous studies have shown that structure and function of RNA motifs can be highly context sensitive to the flanking sequence surrounding them. However, in what ways different flanking sequences influence the structure of an RNA motif they surround has yet to be studied in detail. We focus on a hairpin-rich region of the RNA genome of bacteriophage MS2-a well-studied RNA virus with a wide potential for use in biotechnology-and systematically examine context-dependent structural stability of 14 previously identified hairpin motifs, which include putative and confirmed packaging signals. Combining secondary and tertiary RNA structure prediction of the hairpin motifs placed in different contexts, ranging from the native genomic sequence to random RNA sequences and unstructured poly-U sequences, we determine different measures of motif structural stability. In this way, we show that while some motif structures can be stable in any context, others require specific context provided by the genome. Our results demonstrate the importance of context in RNA structure formation and how changes in the flanking sequence of an RNA motif sometimes lead to drastic changes in its structure. Structural stability of a motif in different contexts could provide additional insights into its functionality as well as assist in determining whether it remains functional when intentionally placed in other contexts.
Collapse
Affiliation(s)
- Veronika Bukina
- Department of Theoretical Physics, Jožef Stefan Institute, Ljubljana, Slovenia; Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Ljubljana, Slovenia
| | - Anže Božič
- Department of Theoretical Physics, Jožef Stefan Institute, Ljubljana, Slovenia.
| |
Collapse
|
9
|
Wang YF, Wang YD, Gao S, Sun W. Implications of p53 in mitochondrial dysfunction and Parkinson's disease. Int J Neurosci 2024; 134:906-917. [PMID: 36514978 DOI: 10.1080/00207454.2022.2158824] [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: 10/26/2022] [Revised: 12/02/2022] [Accepted: 12/05/2022] [Indexed: 12/15/2022]
Abstract
Purpose: To study the underlying molecular mechanisms of p53 in the mitochondrial dysfunction and the pathogenesis of Parkinson's disease (PD), and provide a potential therapeutic target for PD treatment. Methods: We review the contributions of p53 to mitochondrial changes leading to apoptosis and the subsequent degeneration of dopaminergic neurons in PD. Results: P53 is a multifunctional protein implicated in the regulation of diverse cellular processes via transcription-dependent and transcription-independent mechanisms. Mitochondria are vital subcellular organelles for that maintain cellular function, and mitochondrial defect and impairment are primary causes of dopaminergic neuron degeneration in PD. Increasing evidence has revealed that mitochondrial dysfunction-associated dopaminergic neuron degeneration is tightly regulated by p53 in PD pathogenesis. Neurodegenerative stress triggers p53 activation, which induces mitochondrial changes, including transmembrane permeability, reactive oxygen species production, Ca2+ overload, electron transport chain defects and other dynamic alterations, and these changes contribute to neurodegeneration and are linked closely with PD occurrence and development. P53 inhibition has been shown to attenuate mitochondrial dysfunction and protect dopaminergic neurons from degeneration under conditions of neurodegenerative stress. Conclusions: p53 appears to be a potential target for neuroprotective therapy of PD.
Collapse
Affiliation(s)
- Yi-Fan Wang
- Department of Neurology, Shenzhen Sami Medical Center, Shenzhen, China
| | - Ying-Di Wang
- Department of Urinary Surgery, Tumor Hospital of Jilin Province, Chang Chun, China
| | - Song Gao
- Department of Anesthesiology, Tumor Hospital of Jilin Province, Chang Chun, China
| | - Wei Sun
- Department of Neurology, Shenzhen Sami Medical Center, Shenzhen, China
| |
Collapse
|
10
|
Heuchel A, Emblem Å, Jørgensen TE, Moum T, Johansen SD. The Mitogenome of the Subarctic Octocoral Alcyonium digitatum Reveals a Putative tRNA Pro Gene Nested within MutS. Curr Issues Mol Biol 2024; 46:8104-8110. [PMID: 39194696 DOI: 10.3390/cimb46080479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 07/24/2024] [Accepted: 07/25/2024] [Indexed: 08/29/2024] Open
Abstract
We sequenced and analyzed the complete mitogenome of a Norwegian isolate of the octocoral Alcyonium digitatum using the Ion Torrent sequencing technology. The 18,790 bp circular mitochondrial genome was found to harbor the same set of 17 genes, which encode 14 protein subunits, two structural ribosomal RNAs and one tRNA, as reported in other octocorals. In addition, we detected a new tRNAPro-like gene sequence nested within the MutS protein coding region. This putative tRNA gene feature appears to be conserved among the octocorals but has not been reported previously. The A. digitatum mitogenome was also shown to harbor an optional gene (ORFA) that encodes a putative protein of 191 amino acids with unknown function. A mitogenome-based phylogenetic analysis, presented as a maximum likelihood tree, showed that A. digitatum clustered with high statistical confidence with two other Alcyonium species endemic to the Mediterranean Sea and the Southeast Pacific Ocean.
Collapse
Affiliation(s)
- Alisa Heuchel
- Genomic Division, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
- Abisko Scientific Research Station, Swedish Polar Research Secretariat, SE-981 07 Abisko, Sweden
| | - Åse Emblem
- Research Laboratory, Nordland Hospital Trust, 8005 Bodø, Norway
| | - Tor Erik Jørgensen
- Genomic Division, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - Truls Moum
- Genomic Division, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - Steinar Daae Johansen
- Genomic Division, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| |
Collapse
|
11
|
Moran JC, Brivanlou A, Brischigliaro M, Fontanesi F, Rouskin S, Barrientos A. The human mitochondrial mRNA structurome reveals mechanisms of gene expression. Science 2024; 385:eadm9238. [PMID: 39024447 DOI: 10.1126/science.adm9238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 05/24/2024] [Indexed: 07/20/2024]
Abstract
The human mitochondrial genome encodes crucial oxidative phosphorylation system proteins, pivotal for aerobic energy transduction. They are translated from nine monocistronic and two bicistronic transcripts whose native structures remain unexplored, posing a gap in understanding mitochondrial gene expression. In this work, we devised the mitochondrial dimethyl sulfate mutational profiling with sequencing (mitoDMS-MaPseq) method and applied detection of RNA folding ensembles using expectation-maximization (DREEM) clustering to unravel the native mitochondrial messenger RNA (mt-mRNA) structurome in wild-type (WT) and leucine-rich pentatricopeptide repeat-containing protein (LRPPRC)-deficient cells. Our findings elucidate LRPPRC's role as a holdase contributing to maintaining mt-mRNA folding and efficient translation. mt-mRNA structural insights in WT mitochondria, coupled with metabolic labeling, unveil potential mRNA-programmed translational pausing and a distinct programmed ribosomal frameshifting mechanism. Our data define a critical layer of mitochondrial gene expression regulation. These mt-mRNA folding maps provide a reference for studying mt-mRNA structures in diverse physiological and pathological contexts.
Collapse
Affiliation(s)
- J Conor Moran
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, 1600 NW 10th Avenue, Miami, FL 33136, USA
- University of Miami Medical Scientist Training Program, University of Miami Miller School of Medicine, 1600 NW 10th Avenue, Miami, FL 33136, USA
| | - Amir Brivanlou
- Department of Microbiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Michele Brischigliaro
- Department of Neurology, University of Miami Miller School of Medicine, 1600 NW 10th Avenue, Miami, FL 33136, USA
| | - Flavia Fontanesi
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, 1600 NW 10th Avenue, Miami, FL 33136, USA
| | - Silvi Rouskin
- Department of Microbiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Antoni Barrientos
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, 1600 NW 10th Avenue, Miami, FL 33136, USA
- Department of Neurology, University of Miami Miller School of Medicine, 1600 NW 10th Avenue, Miami, FL 33136, USA
- The Miami Veterans Affairs (VA) Medical System, 1201 NW 16th Street, Miami, FL 33125, USA
| |
Collapse
|
12
|
Clarke A, Trujillo A, Mandujano A, Fernandez AG, Chambers A, Ruiz Nunez A, Contreras A, Cuevas B, Collins C, Trujillo CB, Dominguez-Trejo CL, Bustamante DE, Pantoja-Garcia E, Anguiano E, Alcaraz ED, Rodriguez F, Mora FC, Tinoco Rivera F, Cabrera Luis G, Nava HB, Huynh HN, Diaz JC, Hughey JR, Do J, Sevilla JS, Llaja JC, Lopez J, Rosas J, Perez J, Oyola JE, Carrion JV, Black JJ, Chavez JF, Barboza JI, Rodriguez Cortes JP, Barrett KL, Prescott LE, Alvarez L, Merino Juarez L, Velasquez-Moreno MJ, Marquez-Gonzalez MI, Aguirre Linares M, Chavez-Huigo M, Calderon MS, Brambila M, Villa M, Windham MJ, Perez M, Trujillo N, Chenevert P, Lewis P, Guiop P, Mubarz RY, Garcia Velazquez R, Ayala-Tocto RY, Santos S, Fernandez-Güimac SLJ, Zalasar SR, Aguilar-Trauco SE, Duran S, Solis S, Meza SL, Al-Zuhairi T, Padilla VM, Olano YM, Alfaro Maldonado Y. Complete mitochondrial genome of the introduced Indian walking stick Carausius morosus (Lonchodidae, Insecta) from California. Microbiol Resour Announc 2024; 13:e0032124. [PMID: 38819140 PMCID: PMC11256777 DOI: 10.1128/mra.00321-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 05/09/2024] [Indexed: 06/01/2024] Open
Abstract
We present the complete mitochondrial genome of Carausius morosus from Salinas, CA. The mitochondrial genome of C. morosus is circular, AT rich (78.1%), and 16,671 bp in length. It consists of 13 protein-coding, 22 transfer RNA, and 2 ribosomal RNA genes and is identical in gene content to Carausius sp.
Collapse
Affiliation(s)
- Aiden Clarke
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Alice Trujillo
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Andres Mandujano
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Angelica G. Fernandez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Aniyah Chambers
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Areli Ruiz Nunez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Audri Contreras
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Benny Cuevas
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Caitlin Collins
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Christian B. Trujillo
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | | | - Danilo E. Bustamante
- Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva (INDES-CES), Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Amazonas, Peru
- Instituto de Investigación en Ingeniería Ambiental (INAM), Facultad de Ingeniería Civil y Ambiental (FICIAM), Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Amazonas, Peru
| | - Eduardo Pantoja-Garcia
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Elizabeth Anguiano
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Emily D. Alcaraz
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Felipe Rodriguez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Flavio C. Mora
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Froylan Tinoco Rivera
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Gladys Cabrera Luis
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Hailey B. Nava
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Henry N. Huynh
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Javier C. Diaz
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Jeffery R. Hughey
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Jenny Do
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Jeriel S. Sevilla
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Jessica C. Llaja
- Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva (INDES-CES), Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Amazonas, Peru
- Instituto de Investigación en Ingeniería Ambiental (INAM), Facultad de Ingeniería Civil y Ambiental (FICIAM), Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Amazonas, Peru
| | - Jessica Lopez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Jesus Rosas
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Jhordy Perez
- Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva (INDES-CES), Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Amazonas, Peru
| | - Johann E. Oyola
- Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva (INDES-CES), Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Amazonas, Peru
- Instituto de Investigación en Ingeniería Ambiental (INAM), Facultad de Ingeniería Civil y Ambiental (FICIAM), Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Amazonas, Peru
| | - Jois V. Carrion
- Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva (INDES-CES), Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Amazonas, Peru
| | - Joni J. Black
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Jorge F. Chavez
- Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva (INDES-CES), Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Amazonas, Peru
| | - José I. Barboza
- Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva (INDES-CES), Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Amazonas, Peru
| | | | - Konnor L. Barrett
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Lacey E. Prescott
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Layla Alvarez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Lizbet Merino Juarez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | | | | | - Mariana Aguirre Linares
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Maricela Chavez-Huigo
- Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva (INDES-CES), Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Amazonas, Peru
| | - Martha S. Calderon
- Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva (INDES-CES), Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Amazonas, Peru
- Instituto de Investigación en Ingeniería Ambiental (INAM), Facultad de Ingeniería Civil y Ambiental (FICIAM), Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Amazonas, Peru
| | - Mateo Brambila
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Maximiliano Villa
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Mia J. Windham
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Michael Perez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Natalie Trujillo
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Pearl Chenevert
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Phoebe Lewis
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Pilar Guiop
- Instituto de Investigación en Ingeniería Ambiental (INAM), Facultad de Ingeniería Civil y Ambiental (FICIAM), Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Amazonas, Peru
| | - Reema Y. Mubarz
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | | | - Rosmery Y. Ayala-Tocto
- Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva (INDES-CES), Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Amazonas, Peru
| | - Samantha Santos
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Samia L. J. Fernandez-Güimac
- Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva (INDES-CES), Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Amazonas, Peru
- Instituto de Investigación en Ingeniería Ambiental (INAM), Facultad de Ingeniería Civil y Ambiental (FICIAM), Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Amazonas, Peru
| | - Sandra R. Zalasar
- Instituto de Investigación en Ingeniería Ambiental (INAM), Facultad de Ingeniería Civil y Ambiental (FICIAM), Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Amazonas, Peru
| | - Smith E. Aguilar-Trauco
- Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva (INDES-CES), Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Amazonas, Peru
| | - Soledad Duran
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Stephanie Solis
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Steven L. Meza
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Taym Al-Zuhairi
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Victor M. Padilla
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - Yadhira M. Olano
- Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva (INDES-CES), Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Amazonas, Peru
| | - Yareli Alfaro Maldonado
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
| | - on behalf of Hartnell College Genomics Group
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, California, USA
- Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva (INDES-CES), Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Amazonas, Peru
- Instituto de Investigación en Ingeniería Ambiental (INAM), Facultad de Ingeniería Civil y Ambiental (FICIAM), Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Amazonas, Peru
| |
Collapse
|
13
|
He Y, Zhao H, Wang Y, Qu C, Gao X, Miao J. A novel deep-benthic sea cucumber species of Benthodytes (Holothuroidea, Elasipodida, Psychropotidae) and its comprehensive mitochondrial genome sequencing and evolutionary analysis. BMC Genomics 2024; 25:689. [PMID: 39003448 PMCID: PMC11245801 DOI: 10.1186/s12864-024-10607-5] [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: 04/12/2024] [Accepted: 07/09/2024] [Indexed: 07/15/2024] Open
Abstract
BACKGROUND The holothurians, commonly known as sea cucumbers, are marine organisms that possess significant dietary, nutritional, and medicinal value. However, the National Center for Biotechnology Information (NCBI) currently possesses only approximately 70 complete mitochondrial genome datasets of Holothurioidea, which poses limitations on conducting comprehensive research on their genetic resources and evolutionary patterns. In this study, a novel species of sea cucumber belonging to the genus Benthodytes, was discovered in the western Pacific Ocean. The genomic DNA of the novel sea cucumber was extracted, sequenced, assembled and subjected to thorough analysis. RESULTS The mtDNA of Benthodytes sp. Gxx-2023 (GenBank No. OR992091) exhibits a circular structure spanning 17,386 bp, comprising of 13 protein-coding genes (PCGs), 24 non-coding RNAs (2 rRNA genes and 22 tRNA genes), along with two putative control regions measuring 882 bp and 1153 bp, respectively. It exhibits a high AT% content and negative AT-skew, which distinguishing it from the majority of sea cucumbers in terms of environmental adaptability evolution. The mitochondrial gene homology between Gxx-2023 and other sea cucumbers is significantly low, with less than 91% similarity to Benthodytes marianensis, which exhibits the highest level of homology. Additionally, its homology with other sea cucumbers is below 80%. The mitogenome of this species exhibits a unique pattern in terms of start and stop codons, featuring only two types of start codons (ATG and ATT) and three types of stop codons including the incomplete T. Notably, the abundance of AT in the Second position of the codons surpasses that of the First and Third position. The gene arrangement of PCGs exhibits a relatively conserved pattern, while there exists substantial variability in tRNA. Evolutionary analysis revealed that it formed a distinct cluster with B. marianensis and exhibited relatively distant phylogenetic relationships with other sea cucumbers. CONCLUSIONS These findings contribute to the taxonomic diversity of sea cucumbers in the Elasipodida order, thereby holding significant implications for the conservation of biological genetic resources, evolutionary advancements, and the exploration of novel sea cucumber resources.
Collapse
Affiliation(s)
- Yingying He
- Marine Natural Products Research and Development Laboratory, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
- Marine Functional Food Technology Innovation Center of Shandong Province, Rongcheng, 264306, China
| | - Hancheng Zhao
- Marine Natural Products Research and Development Laboratory, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Yongxin Wang
- College of Chemistry and Chemical Engineering, Qingdao University, Qingdao, 266071, China
| | - Changfeng Qu
- Marine Natural Products Research and Development Laboratory, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao Marine Science and Technology Center, Qingdao, 266237, China
- Marine Functional Food Technology Innovation Center of Shandong Province, Rongcheng, 264306, China
| | | | - Jinlai Miao
- Marine Natural Products Research and Development Laboratory, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China.
- Laboratory for Marine Drugs and Bioproducts, Qingdao Marine Science and Technology Center, Qingdao, 266237, China.
- Marine Functional Food Technology Innovation Center of Shandong Province, Rongcheng, 264306, China.
| |
Collapse
|
14
|
Zhang CH, Wang HY, Wang Y, Chi ZH, Liu YS, Zu GH. The first two complete mitochondrial genomes for the genus Anagyrus (Hymenoptera, Encyrtidae) and their phylogenetic implications. Zookeys 2024; 1206:81-98. [PMID: 39006402 PMCID: PMC11245640 DOI: 10.3897/zookeys.1206.121923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 06/12/2024] [Indexed: 07/16/2024] Open
Abstract
Anagyrus, a genus of Encyrtidae (Hymenoptera, Chalcidoidea), represents a successful group of parasitoid insects that attack various mealybug pests of agricultural and forestry plants. Until now, only 20 complete mitochondrial genomes have been sequenced, including those in this study. To enrich the diversity of mitochondrial genomes in Encyrtidae and to gain insights into their phylogenetic relationships, the mitochondrial genomes of two species of Anagyrus were sequenced, and the mitochondrial genomes of these species were compared and analyzed. Encyrtid mitochondrial genomes exhibit similarities in nucleotide composition, gene organization, and control region patterns. Comparative analysis of protein-coding genes revealed varying molecular evolutionary rates among different genes, with six genes (ATP8, ND2, ND4L, ND6, ND4 and ND5) showing higher rates than others. A phylogenetic analysis based on mitochondrial genome sequences supports the monophyly of Encyrtidae; however, the two subfamilies, Encyrtinae and Tetracneminae, are non-monophyletic. This study provides valuable insights into the phylogenetic relationships within the Encyrtidae and underscores the utility of mitochondrial genomes in the systematics of this family.
Collapse
Affiliation(s)
- Cheng-Hui Zhang
- College of Horticulture and Landscape, Tianjin Agricultural University, Tianjin 300392, ChinaTianjin Agricultural UniversityTianjinChina
| | - Hai-Yang Wang
- College of Horticulture and Landscape, Tianjin Agricultural University, Tianjin 300392, ChinaTianjin Agricultural UniversityTianjinChina
| | - Yan Wang
- College of Horticulture and Landscape, Tianjin Agricultural University, Tianjin 300392, ChinaTianjin Agricultural UniversityTianjinChina
| | - Zhi-Hao Chi
- College of Horticulture and Landscape, Tianjin Agricultural University, Tianjin 300392, ChinaTianjin Agricultural UniversityTianjinChina
| | - Yue-Shuo Liu
- College of Horticulture and Landscape, Tianjin Agricultural University, Tianjin 300392, ChinaTianjin Agricultural UniversityTianjinChina
| | - Guo-Hao Zu
- College of Horticulture and Landscape, Tianjin Agricultural University, Tianjin 300392, ChinaTianjin Agricultural UniversityTianjinChina
| |
Collapse
|
15
|
da Silva FS, do Nascimento BLS, Cruz ACR, da Silva SP, Aragão CF, Dias DD, Silva LHDSE, Reis LAM, Reis HCF, Chagas LLD, Rosa Jr. JW, Vieira DBR, Brandão RCF, Medeiros DBDA, Nunes Neto JP. Sequencing and Description of the Mitochondrial Genome of Orthopodomyia fascipes (Diptera: Culicidae). Genes (Basel) 2024; 15:874. [PMID: 39062653 PMCID: PMC11276460 DOI: 10.3390/genes15070874] [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: 05/03/2024] [Revised: 06/03/2024] [Accepted: 06/04/2024] [Indexed: 07/28/2024] Open
Abstract
The genus Orthopodomyia Theobald, 1904 (Diptera: Culicidae) comprises 36 wild mosquito species, with distribution largely restricted to tropical and temperate areas, most of which are not recognized as vectors of epidemiological importance due to the lack of information related to their bionomy and involvement in the cycle transmission of infectious agents. Furthermore, their evolutionary relationships are not completely understood, reflecting the scarcity of genetic information about the genus. Therefore, in this study, we report the first complete description of the mitochondrial genome of a Neotropical species representing the genus, Orthopodomyia fascipes Coquillet, 1906, collected in the Brazilian Amazon region. Using High Throughput Sequencing, we obtained a mitochondrial sequence of 15,598 bp, with an average coverage of 418.5×, comprising 37 functional subunits and a final portion rich in A + T, corresponding to the control region. The phylogenetic analysis, using Maximum Likelihood and Bayesian Inference based on the 13 protein-coding genes, corroborated the monophyly of Culicidae and its two subfamilies, supporting the proximity between the tribes Orthopodomyiini and Mansoniini, partially disagreeing with previous studies based on the use of molecular and morphological markers. The information generated in this study contributes to a better understanding of the taxonomy and evolutionary history of the genus and other groups of Culicidae.
Collapse
Affiliation(s)
- Fábio Silva da Silva
- Graduate Program in Parasitary Biology in the Amazon Region, Center of Biological and Health Sciences, State University of Pará, Belém 66095-663, Brazil; (F.S.d.S.); (A.C.R.C.); (D.D.D.); (L.H.d.S.e.S.); (L.A.M.R.); (H.C.F.R.); (D.B.d.A.M.)
- Evandro Chagas Institute—IEC/MS/SVSA, Department of Arbovirology and Hemorragic Fevers, Ananindeua 67030-000, Brazil; (B.L.S.d.N.); (S.P.d.S.); (C.F.A.); (L.L.d.C.); (J.W.R.J.); (D.B.R.V.); (R.C.F.B.)
| | - Bruna Laís Sena do Nascimento
- Evandro Chagas Institute—IEC/MS/SVSA, Department of Arbovirology and Hemorragic Fevers, Ananindeua 67030-000, Brazil; (B.L.S.d.N.); (S.P.d.S.); (C.F.A.); (L.L.d.C.); (J.W.R.J.); (D.B.R.V.); (R.C.F.B.)
| | - Ana Cecília Ribeiro Cruz
- Graduate Program in Parasitary Biology in the Amazon Region, Center of Biological and Health Sciences, State University of Pará, Belém 66095-663, Brazil; (F.S.d.S.); (A.C.R.C.); (D.D.D.); (L.H.d.S.e.S.); (L.A.M.R.); (H.C.F.R.); (D.B.d.A.M.)
- Evandro Chagas Institute—IEC/MS/SVSA, Department of Arbovirology and Hemorragic Fevers, Ananindeua 67030-000, Brazil; (B.L.S.d.N.); (S.P.d.S.); (C.F.A.); (L.L.d.C.); (J.W.R.J.); (D.B.R.V.); (R.C.F.B.)
| | - Sandro Patroca da Silva
- Evandro Chagas Institute—IEC/MS/SVSA, Department of Arbovirology and Hemorragic Fevers, Ananindeua 67030-000, Brazil; (B.L.S.d.N.); (S.P.d.S.); (C.F.A.); (L.L.d.C.); (J.W.R.J.); (D.B.R.V.); (R.C.F.B.)
| | - Carine Fortes Aragão
- Evandro Chagas Institute—IEC/MS/SVSA, Department of Arbovirology and Hemorragic Fevers, Ananindeua 67030-000, Brazil; (B.L.S.d.N.); (S.P.d.S.); (C.F.A.); (L.L.d.C.); (J.W.R.J.); (D.B.R.V.); (R.C.F.B.)
| | - Daniel Damous Dias
- Graduate Program in Parasitary Biology in the Amazon Region, Center of Biological and Health Sciences, State University of Pará, Belém 66095-663, Brazil; (F.S.d.S.); (A.C.R.C.); (D.D.D.); (L.H.d.S.e.S.); (L.A.M.R.); (H.C.F.R.); (D.B.d.A.M.)
- Evandro Chagas Institute—IEC/MS/SVSA, Department of Arbovirology and Hemorragic Fevers, Ananindeua 67030-000, Brazil; (B.L.S.d.N.); (S.P.d.S.); (C.F.A.); (L.L.d.C.); (J.W.R.J.); (D.B.R.V.); (R.C.F.B.)
| | - Lucas Henrique da Silva e Silva
- Graduate Program in Parasitary Biology in the Amazon Region, Center of Biological and Health Sciences, State University of Pará, Belém 66095-663, Brazil; (F.S.d.S.); (A.C.R.C.); (D.D.D.); (L.H.d.S.e.S.); (L.A.M.R.); (H.C.F.R.); (D.B.d.A.M.)
- Evandro Chagas Institute—IEC/MS/SVSA, Department of Arbovirology and Hemorragic Fevers, Ananindeua 67030-000, Brazil; (B.L.S.d.N.); (S.P.d.S.); (C.F.A.); (L.L.d.C.); (J.W.R.J.); (D.B.R.V.); (R.C.F.B.)
| | - Lúcia Aline Moura Reis
- Graduate Program in Parasitary Biology in the Amazon Region, Center of Biological and Health Sciences, State University of Pará, Belém 66095-663, Brazil; (F.S.d.S.); (A.C.R.C.); (D.D.D.); (L.H.d.S.e.S.); (L.A.M.R.); (H.C.F.R.); (D.B.d.A.M.)
- Evandro Chagas Institute—IEC/MS/SVSA, Department of Arbovirology and Hemorragic Fevers, Ananindeua 67030-000, Brazil; (B.L.S.d.N.); (S.P.d.S.); (C.F.A.); (L.L.d.C.); (J.W.R.J.); (D.B.R.V.); (R.C.F.B.)
| | - Hanna Carolina Farias Reis
- Graduate Program in Parasitary Biology in the Amazon Region, Center of Biological and Health Sciences, State University of Pará, Belém 66095-663, Brazil; (F.S.d.S.); (A.C.R.C.); (D.D.D.); (L.H.d.S.e.S.); (L.A.M.R.); (H.C.F.R.); (D.B.d.A.M.)
- Evandro Chagas Institute—IEC/MS/SVSA, Department of Arbovirology and Hemorragic Fevers, Ananindeua 67030-000, Brazil; (B.L.S.d.N.); (S.P.d.S.); (C.F.A.); (L.L.d.C.); (J.W.R.J.); (D.B.R.V.); (R.C.F.B.)
| | - Liliane Leal das Chagas
- Evandro Chagas Institute—IEC/MS/SVSA, Department of Arbovirology and Hemorragic Fevers, Ananindeua 67030-000, Brazil; (B.L.S.d.N.); (S.P.d.S.); (C.F.A.); (L.L.d.C.); (J.W.R.J.); (D.B.R.V.); (R.C.F.B.)
| | - José Wilson Rosa Jr.
- Evandro Chagas Institute—IEC/MS/SVSA, Department of Arbovirology and Hemorragic Fevers, Ananindeua 67030-000, Brazil; (B.L.S.d.N.); (S.P.d.S.); (C.F.A.); (L.L.d.C.); (J.W.R.J.); (D.B.R.V.); (R.C.F.B.)
| | - Durval Bertram Rodrigues Vieira
- Evandro Chagas Institute—IEC/MS/SVSA, Department of Arbovirology and Hemorragic Fevers, Ananindeua 67030-000, Brazil; (B.L.S.d.N.); (S.P.d.S.); (C.F.A.); (L.L.d.C.); (J.W.R.J.); (D.B.R.V.); (R.C.F.B.)
| | - Roberto Carlos Feitosa Brandão
- Evandro Chagas Institute—IEC/MS/SVSA, Department of Arbovirology and Hemorragic Fevers, Ananindeua 67030-000, Brazil; (B.L.S.d.N.); (S.P.d.S.); (C.F.A.); (L.L.d.C.); (J.W.R.J.); (D.B.R.V.); (R.C.F.B.)
| | - Daniele Barbosa de Almeida Medeiros
- Graduate Program in Parasitary Biology in the Amazon Region, Center of Biological and Health Sciences, State University of Pará, Belém 66095-663, Brazil; (F.S.d.S.); (A.C.R.C.); (D.D.D.); (L.H.d.S.e.S.); (L.A.M.R.); (H.C.F.R.); (D.B.d.A.M.)
- Evandro Chagas Institute—IEC/MS/SVSA, Department of Arbovirology and Hemorragic Fevers, Ananindeua 67030-000, Brazil; (B.L.S.d.N.); (S.P.d.S.); (C.F.A.); (L.L.d.C.); (J.W.R.J.); (D.B.R.V.); (R.C.F.B.)
| | - Joaquim Pinto Nunes Neto
- Graduate Program in Parasitary Biology in the Amazon Region, Center of Biological and Health Sciences, State University of Pará, Belém 66095-663, Brazil; (F.S.d.S.); (A.C.R.C.); (D.D.D.); (L.H.d.S.e.S.); (L.A.M.R.); (H.C.F.R.); (D.B.d.A.M.)
- Evandro Chagas Institute—IEC/MS/SVSA, Department of Arbovirology and Hemorragic Fevers, Ananindeua 67030-000, Brazil; (B.L.S.d.N.); (S.P.d.S.); (C.F.A.); (L.L.d.C.); (J.W.R.J.); (D.B.R.V.); (R.C.F.B.)
| |
Collapse
|
16
|
Sanita Lima M, Silva Domingues D, Rossi Paschoal A, Smith DR. Long-read RNA sequencing can probe organelle genome pervasive transcription. Brief Funct Genomics 2024:elae026. [PMID: 38880995 DOI: 10.1093/bfgp/elae026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/20/2024] [Accepted: 05/30/2024] [Indexed: 06/18/2024] Open
Abstract
40 years ago, organelle genomes were assumed to be streamlined and, perhaps, unexciting remnants of their prokaryotic past. However, the field of organelle genomics has exposed an unparallel diversity in genome architecture (i.e. genome size, structure, and content). The transcription of these eccentric genomes can be just as elaborate - organelle genomes are pervasively transcribed into a plethora of RNA types. However, while organelle protein-coding genes are known to produce polycistronic transcripts that undergo heavy posttranscriptional processing, the nature of organelle noncoding transcriptomes is still poorly resolved. Here, we review how wet-lab experiments and second-generation sequencing data (i.e. short reads) have been useful to determine certain types of organelle RNAs, particularly noncoding RNAs. We then explain how third-generation (long-read) RNA-Seq data represent the new frontier in organelle transcriptomics. We show that public repositories (e.g. NCBI SRA) already contain enough data for inter-phyla comparative studies and argue that organelle biologists can benefit from such data. We discuss the prospects of using publicly available sequencing data for organelle-focused studies and examine the challenges of such an approach. We highlight that the lack of a comprehensive database dedicated to organelle genomics/transcriptomics is a major impediment to the development of a field with implications in basic and applied science.
Collapse
Affiliation(s)
- Matheus Sanita Lima
- Department of Biology, Western University, 1151 Richmond Street, London, Ontario N6A 5B7, Canada
| | - Douglas Silva Domingues
- Department of Genetics, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Avenida Padua Dias 11, Piracicaba, SP 13418-900, Brazil
| | - Alexandre Rossi Paschoal
- Department of Computer Science, Bioinformatics and Pattern Recognition Group (BIOINFO-CP), Federal University of Technology - Paraná - UTFPR, Avenida Alberto Carazzai 1640, Cornélio Procópio, PR 86300000, Brazil
| | - David Roy Smith
- Department of Biology, Western University, 1151 Richmond Street, London, Ontario N6A 5B7, Canada
| |
Collapse
|
17
|
Siddika MA, Ahmed KA, Alam MS, Bushra J, Begum RA. Complete mitogenome and intra-family comparative mitogenomics showed distinct position of Pama Croaker Otolithoides pama. Sci Rep 2024; 14:13820. [PMID: 38879694 PMCID: PMC11180200 DOI: 10.1038/s41598-024-64791-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 06/13/2024] [Indexed: 06/19/2024] Open
Abstract
The Pama Croaker, Otolithoides pama, is an economically important fish species in Bangladesh. Intra-family similarities in morphology and typical barcode sequences of cox1 create ambiguities in its identification. Therefore, morphology and the complete mitochondrial genome of O. pama, and comparative mitogenomics within the family Sciaenidae have been studied. Extracted genomic DNA was subjected to Illumina-based short read sequencing for De-Novo mitogenome assembly. The complete mitogenome of O. pama (Accession: OQ784575.1) was 16,513 bp, with strong AC biasness and strand asymmetry. Relative synonymous codon usage (RSCU) among 13 protein-coding genes (PCGs) of O. pama was also analyzed. The studied mitogenomes including O. pama exhibited consistent sizes and gene orders, except for the genus Johnius which possessed notably longer mitogenomes with unique gene rearrangements. Different genetic distance metrics across 30 species of Sciaenidae family demonstrated 12S rRNA and the control region (CR) as the most conserved and variable regions, respectively, while most of the PCGs undergone a purifying selection. Different phylogenetic trees were congruent with one another, where O. pama was distinctly placed. This study would contribute to distinguishing closely related fish species of Sciaenidae family and can be instrumental in conserving the genetic diversity of O. pama.
Collapse
Affiliation(s)
- Most Ayesha Siddika
- Genetics and Molecular Biology Laboratory, Department of Zoology, University of Dhaka, Dhaka, 1000, Bangladesh
| | | | - Mohammad Shamimul Alam
- Genetics and Molecular Biology Laboratory, Department of Zoology, University of Dhaka, Dhaka, 1000, Bangladesh.
| | - Jannatul Bushra
- Genetics and Molecular Biology Laboratory, Department of Zoology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Rowshan Ara Begum
- Genetics and Molecular Biology Laboratory, Department of Zoology, University of Dhaka, Dhaka, 1000, Bangladesh
| |
Collapse
|
18
|
Bedi K, Magnuson B, Narayanan IV, McShane A, Ashaka M, Paulsen MT, Wilson TE, Ljungman M. Isoform and pathway-specific regulation of post-transcriptional RNA processing in human cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.12.598705. [PMID: 38915566 PMCID: PMC11195214 DOI: 10.1101/2024.06.12.598705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Steady-state levels of RNA transcripts are controlled by their rates of synthesis and degradation. Here we used nascent RNA Bru-seq and BruChase-seq to profile RNA dynamics across 16 human cell lines as part of ENCODE4 Deeply Profiled Cell Lines collection. We show that RNA turnover dynamics differ widely between transcripts of different genes and between different classes of RNA. Gene set enrichment analysis (GSEA) revealed that transcripts encoding proteins belonging to the same pathway often show similar turnover dynamics. Furthermore, transcript isoforms show distinct dynamics suggesting that RNA turnover is important in regulating mRNA isoform choice. Finally, splicing across newly made transcripts appears to be cooperative with either all or none type splicing. These data sets generated as part of ENCODE4 illustrate the intricate and coordinated regulation of RNA dynamics in controlling gene expression to allow for the precise coordination of cellular functions.
Collapse
Affiliation(s)
- Karan Bedi
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Brian Magnuson
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Pathology and Department of Human Genetics, University of Michigan Medical School, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Ariel McShane
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mario Ashaka
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Michelle T Paulsen
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Thomas E Wilson
- Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Pathology and Department of Human Genetics, University of Michigan Medical School, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mats Ljungman
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
- Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| |
Collapse
|
19
|
Ku D, Yang Y, Park Y, Jang D, Lee N, Lee YK, Lee K, Lee J, Han YB, Jang S, Choi SR, Ha YJ, Choi YS, Jeong WJ, Lee YJ, Lee KJ, Cha S, Kim Y. SLIRP promotes autoimmune diseases by amplifying antiviral signaling via positive feedback regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.28.587146. [PMID: 38915695 PMCID: PMC11195051 DOI: 10.1101/2024.03.28.587146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
The abnormal innate immune response is a prominent feature underlying autoimmune diseases. One emerging factor that can trigger dysregulated immune activation is cytosolic mitochondrial double-stranded RNAs (mt-dsRNAs). However, the mechanism by which mt-dsRNAs stimulate immune responses remains poorly understood. Here, we discover SRA stem-loop interacting RNA binding protein (SLIRP) as a key amplifier of mt-dsRNA-triggered antiviral signals. In autoimmune diseases, SLIRP is commonly upregulated, and targeted knockdown of SLIRP dampens the interferon response. We find that the activation of melanoma differentiation-associated gene 5 (MDA5) by exogenous dsRNAs upregulates SLIRP, which then stabilizes mt-dsRNAs and promotes their cytosolic release to activate MDA5 further, augmenting the interferon response. Furthermore, the downregulation of SLIRP partially rescues the abnormal interferon-stimulated gene expression in autoimmune patients' primary cells and makes cells vulnerable to certain viral infections. Our study unveils SLIRP as a pivotal mediator of interferon response through positive feedback amplification of antiviral signaling.
Collapse
Affiliation(s)
- Doyeong Ku
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Yewon Yang
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Youngran Park
- Center for RNA Research, Institute of Basic Science, Seoul, 08826, Republic of Korea
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Daesong Jang
- Department of Oral and Maxillofacial Diagnostic Science, Center for Orphaned Autoimmune Disorders, University of Florida College of Dentistry, Gainesville, Florida, 32610, United States of America
| | - Namseok Lee
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Yong-ki Lee
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Keonyong Lee
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Jaeseon Lee
- R&D Institute, ORGANOIDSCIENCES Ltd., Seongnam, 13488, Republic of Korea
| | - Yeon Bi Han
- Department of Pathology and Translational Medicine, Seoul National University Bundang Hospital, Seongnam, 13620, Republic of Korea
| | - Soojin Jang
- R&D Institute, ORGANOIDSCIENCES Ltd., Seongnam, 13488, Republic of Korea
| | - Se Rim Choi
- Division of Rheumatology, Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, 13620, Republic of Korea
| | - You-Jung Ha
- Division of Rheumatology, Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, 13620, Republic of Korea
| | - Yong Seok Choi
- Medical Science Research Institute, Seoul National University Bundang Hospital, Seongnam, 13620, Republic of Korea
| | - Woo-Jin Jeong
- Department of Otorhinolaryngology - Head & Neck Surgery, Seoul National University Bundang Hospital, Seongnam, 13620, Republic of Korea
- Sensory Organ Research Institute, Seoul National University Medical Research Center, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Yun Jong Lee
- Department of Pathology and Translational Medicine, Seoul National University Bundang Hospital, Seongnam, 13620, Republic of Korea
- Division of Rheumatology, Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, 13620, Republic of Korea
| | - Kyung Jin Lee
- R&D Institute, ORGANOIDSCIENCES Ltd., Seongnam, 13488, Republic of Korea
| | - Seunghee Cha
- Department of Oral and Maxillofacial Diagnostic Science, Center for Orphaned Autoimmune Disorders, University of Florida College of Dentistry, Gainesville, Florida, 32610, United States of America
| | - Yoosik Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Graduate School of Engineering Biology, KAIST, Daejeon, 34141, Republic of Korea
- KAIST Institute for BioCentury (KIB), Daejeon, 34141, Republic of Korea
- KAIST Institute for Health Science and Technology (KIHST), Daejeon 34141, Republic of Korea
| |
Collapse
|
20
|
Bernardino Gomes TM, Vincent AE, Menger KE, Stewart JB, Nicholls TJ. Mechanisms and pathologies of human mitochondrial DNA replication and deletion formation. Biochem J 2024; 481:683-715. [PMID: 38804971 PMCID: PMC11346376 DOI: 10.1042/bcj20230262] [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: 03/22/2024] [Revised: 05/13/2024] [Accepted: 05/14/2024] [Indexed: 05/29/2024]
Abstract
Human mitochondria possess a multi-copy circular genome, mitochondrial DNA (mtDNA), that is essential for cellular energy metabolism. The number of copies of mtDNA per cell, and their integrity, are maintained by nuclear-encoded mtDNA replication and repair machineries. Aberrant mtDNA replication and mtDNA breakage are believed to cause deletions within mtDNA. The genomic location and breakpoint sequences of these deletions show similar patterns across various inherited and acquired diseases, and are also observed during normal ageing, suggesting a common mechanism of deletion formation. However, an ongoing debate over the mechanism by which mtDNA replicates has made it difficult to develop clear and testable models for how mtDNA rearrangements arise and propagate at a molecular and cellular level. These deletions may impair energy metabolism if present in a high proportion of the mtDNA copies within the cell, and can be seen in primary mitochondrial diseases, either in sporadic cases or caused by autosomal variants in nuclear-encoded mtDNA maintenance genes. These mitochondrial diseases have diverse genetic causes and multiple modes of inheritance, and show notoriously broad clinical heterogeneity with complex tissue specificities, which further makes establishing genotype-phenotype relationships challenging. In this review, we aim to cover our current understanding of how the human mitochondrial genome is replicated, the mechanisms by which mtDNA replication and repair can lead to mtDNA instability in the form of large-scale rearrangements, how rearranged mtDNAs subsequently accumulate within cells, and the pathological consequences when this occurs.
Collapse
Affiliation(s)
- Tiago M. Bernardino Gomes
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- NHS England Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4HH, U.K
| | - Amy E. Vincent
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | - Katja E. Menger
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | - James B. Stewart
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | - Thomas J. Nicholls
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| |
Collapse
|
21
|
Pang S, Zhang Q, Liang L, Qin Y, Li S, Bian X. Comparative Mitogenomics and Phylogenetic Implications for Nine Species of the Subfamily Meconematinae (Orthoptera: Tettigoniidae). INSECTS 2024; 15:413. [PMID: 38921128 PMCID: PMC11204050 DOI: 10.3390/insects15060413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/30/2024] [Accepted: 05/31/2024] [Indexed: 06/27/2024]
Abstract
Currently, the subfamily Meconematinae encompasses 1029 species, but whole-mitochondrial-genome assemblies have only been made available for 13. In this study, the whole mitochondrial genomes (mitogenomes) of nine additional species in the subfamily Meconematinae were sequenced. The size ranged from 15,627 bp to 17,461 bp, indicating double-stranded circular structures. The length of the control region was the main cause of the difference in mitochondrial genome length among the nine species. All the mitogenomes including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs) and a control region (CR). The majority strand encoded 23 genes, and the minority strand encoded 14 genes. A phylogenetic analysis reaffirmed the monophyletic status of each subfamily, but the monophysitism of Xizicus, Xiphidiopsis and Phlugiolopsis was not supported.
Collapse
Affiliation(s)
- Siyu Pang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin 541006, China; (S.P.); (Q.Z.); (L.L.); (Y.Q.); (S.L.)
- College of Life Sciences, Guangxi Normal University, Guilin 541006, China
| | - Qianwen Zhang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin 541006, China; (S.P.); (Q.Z.); (L.L.); (Y.Q.); (S.L.)
- College of Life Sciences, Guangxi Normal University, Guilin 541006, China
| | - Lili Liang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin 541006, China; (S.P.); (Q.Z.); (L.L.); (Y.Q.); (S.L.)
- College of Life Sciences, Guangxi Normal University, Guilin 541006, China
| | - Yanting Qin
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin 541006, China; (S.P.); (Q.Z.); (L.L.); (Y.Q.); (S.L.)
- College of Life Sciences, Guangxi Normal University, Guilin 541006, China
| | - Shan Li
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin 541006, China; (S.P.); (Q.Z.); (L.L.); (Y.Q.); (S.L.)
- College of Life Sciences, Guangxi Normal University, Guilin 541006, China
| | - Xun Bian
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin 541006, China; (S.P.); (Q.Z.); (L.L.); (Y.Q.); (S.L.)
- College of Life Sciences, Guangxi Normal University, Guilin 541006, China
| |
Collapse
|
22
|
Meynier V, Hardwick SW, Catala M, Roske JJ, Oerum S, Chirgadze DY, Barraud P, Yue WW, Luisi BF, Tisné C. Structural basis for human mitochondrial tRNA maturation. Nat Commun 2024; 15:4683. [PMID: 38824131 PMCID: PMC11144196 DOI: 10.1038/s41467-024-49132-0] [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: 05/21/2024] [Indexed: 06/03/2024] Open
Abstract
The human mitochondrial genome is transcribed into two RNAs, containing mRNAs, rRNAs and tRNAs, all dedicated to produce essential proteins of the respiratory chain. The precise excision of tRNAs by the mitochondrial endoribonucleases (mt-RNase), P and Z, releases all RNA species from the two RNA transcripts. The tRNAs then undergo 3'-CCA addition. In metazoan mitochondria, RNase P is a multi-enzyme assembly that comprises the endoribonuclease PRORP and a tRNA methyltransferase subcomplex. The requirement for this tRNA methyltransferase subcomplex for mt-RNase P cleavage activity, as well as the mechanisms of pre-tRNA 3'-cleavage and 3'-CCA addition, are still poorly understood. Here, we report cryo-EM structures that visualise four steps of mitochondrial tRNA maturation: 5' and 3' tRNA-end processing, methylation and 3'-CCA addition, and explain the defined sequential order of the tRNA processing steps. The methyltransferase subcomplex recognises the pre-tRNA in a distinct mode that can support tRNA-end processing and 3'-CCA addition, likely resulting from an evolutionary adaptation of mitochondrial tRNA maturation complexes to the structurally-fragile mitochondrial tRNAs. This subcomplex can also ensure a tRNA-folding quality-control checkpoint before the sequential docking of the maturation enzymes. Altogether, our study provides detailed molecular insight into RNA-transcript processing and tRNA maturation in human mitochondria.
Collapse
Affiliation(s)
- Vincent Meynier
- Expression Génétique Microbienne, Université Paris Cité, CNRS, Institut de Biologie Physico-Chimique (IBPC), 75005, Paris, France
| | - Steven W Hardwick
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Marjorie Catala
- Expression Génétique Microbienne, Université Paris Cité, CNRS, Institut de Biologie Physico-Chimique (IBPC), 75005, Paris, France
| | - Johann J Roske
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Stephanie Oerum
- Expression Génétique Microbienne, Université Paris Cité, CNRS, Institut de Biologie Physico-Chimique (IBPC), 75005, Paris, France
| | - Dimitri Y Chirgadze
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Pierre Barraud
- Expression Génétique Microbienne, Université Paris Cité, CNRS, Institut de Biologie Physico-Chimique (IBPC), 75005, Paris, France
| | - Wyatt W Yue
- Centre for Medicines Discovery, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7DQ, UK
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Ben F Luisi
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Carine Tisné
- Expression Génétique Microbienne, Université Paris Cité, CNRS, Institut de Biologie Physico-Chimique (IBPC), 75005, Paris, France.
| |
Collapse
|
23
|
Shah RA, Riyaz M, Ignacimuthu S, Sivasankaran K. Characterization and Molecular Phylogenetic Analysis of Subfamily Erebinae (Lepidoptera: Noctuoidea: Erebidae) Using Five Complete Mitochondrial Genomes. Biochem Genet 2024; 62:2224-2252. [PMID: 37891448 DOI: 10.1007/s10528-023-10528-0] [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: 07/20/2022] [Accepted: 09/07/2023] [Indexed: 10/29/2023]
Abstract
In this study, the complete mitogenomes of Sympis rufibasis, Lacera noctilio, Oxyodes scrobiculata, Mocis undata, and Artena dotata were newly sequenced to bring up-to-date the database using the next-generation sequencing methods. The gene order of all sequenced mitogenomes was identical consisting of 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and a non-coding A+T-rich region, which were common to other Lepidopteran insects. All protein-coding genes (PCGs) initiated with a canonical ATN codon and ended with TAN or an incomplete stop codon, single T. The A+T-rich region of S. rufibasis, L. noctilio, O. scrobiculata, M. undata, and A. dotata are 406 bp, 462 bp, 372 bp, 410 bp, and 406 bp long, respectively, containing number of characteristics that are distinctive to Noctuoidea moths. We analyzed concatenated amino acid sequences of protein-coding genes not including rRNAs, using Maximum Likelihood and Bayesian Inference methods. The phylogenetic analyses indicated that the tribe relationships within Erebinae were reconstructed as (Sypnini+((Erebini 1+Poaphilini 1)+((Euclidiini+Catocalini+(Hypopyrini+Erebini 2))+((Hulodini+(Poaphilini 2+Ophiusini))))). Phylogenetic analyses supported and confirmed the monophyly of the subfamilies' relationships as follows: (Hypeninae+Lymantriinae)+((Scoliopterginae+((Calpinae+Erebinae)+((Herminiinae+Aganainae)+Arctiinae)))) within Erebidae.
Collapse
Affiliation(s)
- Rauf Ahmad Shah
- Division of Taxonomy and Biodiversity, Entomology Research Institute, Loyola Collège, Chennai, Tamil Nadu, 600034, India
| | - Muzafar Riyaz
- Division of Taxonomy and Biodiversity, Entomology Research Institute, Loyola Collège, Chennai, Tamil Nadu, 600034, India
| | - Savarimuthu Ignacimuthu
- Xavier Research Foundation, St. Xavier's College, Palayamkottai, Tamil Nadu, 627002, India
- Creighton University, 2500 California Plaza, Omaha, USA
| | - Kuppusamy Sivasankaran
- Division of Taxonomy and Biodiversity, Entomology Research Institute, Loyola Collège, Chennai, Tamil Nadu, 600034, India.
| |
Collapse
|
24
|
Blackwell AM, Jami-Alahmadi Y, Nasamu AS, Kudo S, Senoo A, Slam C, Tsumoto K, Wohlschlegel JA, Caaveiro JMM, Goldberg DE, Sigala PA. Malaria parasites require a divergent heme oxygenase for apicoplast gene expression and biogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.30.596652. [PMID: 38853871 PMCID: PMC11160694 DOI: 10.1101/2024.05.30.596652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Malaria parasites have evolved unusual metabolic adaptations that specialize them for growth within heme-rich human erythrocytes. During blood-stage infection, Plasmodium falciparum parasites internalize and digest abundant host hemoglobin within the digestive vacuole. This massive catabolic process generates copious free heme, most of which is biomineralized into inert hemozoin. Parasites also express a divergent heme oxygenase (HO)-like protein (PfHO) that lacks key active-site residues and has lost canonical HO activity. The cellular role of this unusual protein that underpins its retention by parasites has been unknown. To unravel PfHO function, we first determined a 2.8 Å-resolution X-ray structure that revealed a highly α-helical fold indicative of distant HO homology. Localization studies unveiled PfHO targeting to the apicoplast organelle, where it is imported and undergoes N-terminal processing but retains most of the electropositive transit peptide. We observed that conditional knockdown of PfHO was lethal to parasites, which died from defective apicoplast biogenesis and impaired isoprenoid-precursor synthesis. Complementation and molecular-interaction studies revealed an essential role for the electropositive N-terminus of PfHO, which selectively associates with the apicoplast genome and enzymes involved in nucleic acid metabolism and gene expression. PfHO knockdown resulted in a specific deficiency in levels of apicoplast-encoded RNA but not DNA. These studies reveal an essential function for PfHO in apicoplast maintenance and suggest that Plasmodium repurposed the conserved HO scaffold from its canonical heme-degrading function in the ancestral chloroplast to fulfill a critical adaptive role in organelle gene expression.
Collapse
Affiliation(s)
| | | | - Armiyaw S. Nasamu
- Departments of Medicine and Molecular Microbiology, Washington University School of Medicine, St. Louis, MO
| | - Shota Kudo
- Department of Chemistry & Biotechnology, The University of Tokyo, Tokyo, Japan
| | - Akinobu Senoo
- Department of Protein Drug Discovery, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Celine Slam
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT
| | - Kouhei Tsumoto
- Department of Chemistry & Biotechnology, The University of Tokyo, Tokyo, Japan
- Department of Bioengineering, University of Tokyo, Tokyo, Japan
| | | | - Jose M. M. Caaveiro
- Department of Chemistry & Biotechnology, The University of Tokyo, Tokyo, Japan
| | - Daniel E. Goldberg
- Departments of Medicine and Molecular Microbiology, Washington University School of Medicine, St. Louis, MO
| | - Paul A. Sigala
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT
- Departments of Medicine and Molecular Microbiology, Washington University School of Medicine, St. Louis, MO
| |
Collapse
|
25
|
Zhang X, Li C, Jiang L, Qiao G, Chen J. Characteristics and Comparative Analysis of Mitochondrial Genomes of the Aphid Genus Hyalopterus Koch (Hemiptera: Aphididae: Aphidinae). INSECTS 2024; 15:389. [PMID: 38921104 PMCID: PMC11204073 DOI: 10.3390/insects15060389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/18/2024] [Accepted: 05/24/2024] [Indexed: 06/27/2024]
Abstract
Using Illumina sequencing technology, we generated complete mitochondrial genomes (mitogenomes) of three constituent species of the aphid genus Hyalopterus Koch, Hyalopterus amygdali (Blanchard), Hyalopterus arundiniformis Ghulamullah, and Hyalopterus pruni (Geoffroy). The sizes of the Hyalopterus mitogenomes range from 15,306 to 15,410 bp, primarily due to variations in the length of non-coding regions. The Hyalopterus mitogenomes consist of 37 coding genes arranged in the order of the ancestral insect mitogenome, a control region, and a repeat region between trnE and trnF. According to the COI-based analysis, one previously reported mitogenome of H. pruni should be assigned to H. arundiniformis. The gene order, nucleotide composition, and codon usage in the Hyalopterus mitogenomes are highly conserved and similar to those of other species of Aphidinae. The tandem repeat units differ in nucleotide composition, length, and copy number across three Hyalopterus species. Within the widespread Eurasian species H. arundiniformis, variation in repeat units among different geographic populations is observed, indicating that the repeat region may provide valuable insights for studying the intraspecific diversification of aphids. Phylogenetic analyses based on 28 complete mitogenomes of Aphidinae supported the monophyly of Aphidinae, Aphidini, Macrosiphini, and two subtribes of Aphidini. Hyalopterus was monophyletic. H. amygdali and H. pruni formed a sister group, while H. arundiniformis was placed basally. Characterization of the mitogenomes of Hyalopterus provides valuable resources for further comparative studies and for advancing our understanding of the aphid mitogenome architecture.
Collapse
Affiliation(s)
- Xiaolu Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (X.Z.); (C.L.); (L.J.)
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cailing Li
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (X.Z.); (C.L.); (L.J.)
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liyun Jiang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (X.Z.); (C.L.); (L.J.)
| | - Gexia Qiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (X.Z.); (C.L.); (L.J.)
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Chen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (X.Z.); (C.L.); (L.J.)
| |
Collapse
|
26
|
Antolínez-Fernández Á, Esteban-Ramos P, Fernández-Moreno MÁ, Clemente P. Molecular pathways in mitochondrial disorders due to a defective mitochondrial protein synthesis. Front Cell Dev Biol 2024; 12:1410245. [PMID: 38855161 PMCID: PMC11157125 DOI: 10.3389/fcell.2024.1410245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 05/09/2024] [Indexed: 06/11/2024] Open
Abstract
Mitochondria play a central role in cellular metabolism producing the necessary ATP through oxidative phosphorylation. As a remnant of their prokaryotic past, mitochondria contain their own genome, which encodes 13 subunits of the oxidative phosphorylation system, as well as the tRNAs and rRNAs necessary for their translation in the organelle. Mitochondrial protein synthesis depends on the import of a vast array of nuclear-encoded proteins including the mitochondrial ribosome protein components, translation factors, aminoacyl-tRNA synthetases or assembly factors among others. Cryo-EM studies have improved our understanding of the composition of the mitochondrial ribosome and the factors required for mitochondrial protein synthesis and the advances in next-generation sequencing techniques have allowed for the identification of a growing number of genes involved in mitochondrial pathologies with a defective translation. These disorders are often multisystemic, affecting those tissues with a higher energy demand, and often present with neurodegenerative phenotypes. In this article, we review the known proteins required for mitochondrial translation, the disorders that derive from a defective mitochondrial protein synthesis and the animal models that have been established for their study.
Collapse
Affiliation(s)
- Álvaro Antolínez-Fernández
- Instituto de Investigaciones Biomédicas Sols-Morreale (IIBM), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Departamento de Bioquímica, Universidad Autónoma de Madrid, Madrid, Spain
| | - Paula Esteban-Ramos
- Instituto de Investigaciones Biomédicas Sols-Morreale (IIBM), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Departamento de Bioquímica, Universidad Autónoma de Madrid, Madrid, Spain
| | - Miguel Ángel Fernández-Moreno
- Instituto de Investigaciones Biomédicas Sols-Morreale (IIBM), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Departamento de Bioquímica, Universidad Autónoma de Madrid, Madrid, Spain
| | - Paula Clemente
- Instituto de Investigaciones Biomédicas Sols-Morreale (IIBM), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Departamento de Bioquímica, Universidad Autónoma de Madrid, Madrid, Spain
| |
Collapse
|
27
|
Koludarova L, Battersby BJ. Mitochondrial protein synthesis quality control. Hum Mol Genet 2024; 33:R53-R60. [PMID: 38280230 PMCID: PMC11112378 DOI: 10.1093/hmg/ddae012] [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: 12/06/2023] [Accepted: 01/05/2023] [Indexed: 01/29/2024] Open
Abstract
Human mitochondrial DNA is one of the most simplified cellular genomes and facilitates compartmentalized gene expression. Within the organelle, there is no physical barrier to separate transcription and translation, nor is there evidence that quality control surveillance pathways are active to prevent translation on faulty mRNA transcripts. Mitochondrial ribosomes synthesize 13 hydrophobic proteins that require co-translational insertion into the inner membrane of the organelle. To maintain the integrity of the inner membrane, which is essential for organelle function, requires responsive quality control mechanisms to recognize aberrations in protein synthesis. In this review, we explore how defects in mitochondrial protein synthesis can arise due to the culmination of inherent mistakes that occur throughout the steps of gene expression. In turn, we examine the stepwise series of quality control processes that are needed to eliminate any mistakes that would perturb organelle homeostasis. We aim to provide an integrated view on the quality control mechanisms of mitochondrial protein synthesis and to identify promising avenues for future research.
Collapse
Affiliation(s)
- Lidiia Koludarova
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki 00014, Finland
| | - Brendan J Battersby
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki 00014, Finland
| |
Collapse
|
28
|
Hughes LA, Rackham O, Filipovska A. Illuminating mitochondrial translation through mouse models. Hum Mol Genet 2024; 33:R61-R79. [PMID: 38779771 PMCID: PMC11112386 DOI: 10.1093/hmg/ddae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 01/22/2024] [Accepted: 01/31/2024] [Indexed: 05/25/2024] Open
Abstract
Mitochondria are hubs of metabolic activity with a major role in ATP conversion by oxidative phosphorylation (OXPHOS). The mammalian mitochondrial genome encodes 11 mRNAs encoding 13 OXPHOS proteins along with 2 rRNAs and 22 tRNAs, that facilitate their translation on mitoribosomes. Maintaining the internal production of core OXPHOS subunits requires modulation of the mitochondrial capacity to match the cellular requirements and correct insertion of particularly hydrophobic proteins into the inner mitochondrial membrane. The mitochondrial translation system is essential for energy production and defects result in severe, phenotypically diverse diseases, including mitochondrial diseases that typically affect postmitotic tissues with high metabolic demands. Understanding the complex mechanisms that underlie the pathologies of diseases involving impaired mitochondrial translation is key to tailoring specific treatments and effectively targeting the affected organs. Disease mutations have provided a fundamental, yet limited, understanding of mitochondrial protein synthesis, since effective modification of the mitochondrial genome has proven challenging. However, advances in next generation sequencing, cryoelectron microscopy, and multi-omic technologies have revealed unexpected and unusual features of the mitochondrial protein synthesis machinery in the last decade. Genome editing tools have generated unique models that have accelerated our mechanistic understanding of mitochondrial translation and its physiological importance. Here we review the most recent mouse models of disease pathogenesis caused by defects in mitochondrial protein synthesis and discuss their value for preclinical research and therapeutic development.
Collapse
Affiliation(s)
- Laetitia A Hughes
- Telethon Kids Institute, Northern Entrance, Perth Children’s Hospital, 15 Hospital Avenue, Nedlands, WA 6009, Australia
- Harry Perkins Institute of Medical Research, 6 Verdun Street, Nedlands, WA 6009, Australia
- ARC Centre of Excellence in Synthetic Biology, 35 Stirling Highway, Crawley, WA 6009, The University of Western Australia, Crawley, WA 6009, Australia
| | - Oliver Rackham
- Telethon Kids Institute, Northern Entrance, Perth Children’s Hospital, 15 Hospital Avenue, Nedlands, WA 6009, Australia
- Harry Perkins Institute of Medical Research, 6 Verdun Street, Nedlands, WA 6009, Australia
- ARC Centre of Excellence in Synthetic Biology, 35 Stirling Highway, Crawley, WA 6009, The University of Western Australia, Crawley, WA 6009, Australia
- Curtin Medical School, Curtin University, Kent Street, Bentley, WA 6102, Australia
- Curtin Health Innovation Research Institute, Curtin University, Kent Street, Bentley, WA 6102, Australia
| | - Aleksandra Filipovska
- Telethon Kids Institute, Northern Entrance, Perth Children’s Hospital, 15 Hospital Avenue, Nedlands, WA 6009, Australia
- ARC Centre of Excellence in Synthetic Biology, 35 Stirling Highway, Crawley, WA 6009, The University of Western Australia, Crawley, WA 6009, Australia
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, 19 Innovation Walk, Clayton, Clayton, VIC 3168, Australia
| |
Collapse
|
29
|
Santonoceto G, Jurkiewicz A, Szczesny RJ. RNA degradation in human mitochondria: the journey is not finished. Hum Mol Genet 2024; 33:R26-R33. [PMID: 38779774 DOI: 10.1093/hmg/ddae043] [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: 01/04/2024] [Revised: 03/03/2024] [Accepted: 03/05/2024] [Indexed: 05/25/2024] Open
Abstract
Mitochondria are vital organelles present in almost all eukaryotic cells. Although most of the mitochondrial proteins are nuclear-encoded, mitochondria contain their own genome, whose proper expression is necessary for mitochondrial function. Transcription of the human mitochondrial genome results in the synthesis of long polycistronic transcripts that are subsequently processed by endonucleases to release individual RNA molecules, including precursors of sense protein-encoding mRNA (mt-mRNA) and a vast amount of antisense noncoding RNAs. Because of mitochondrial DNA (mtDNA) organization, the regulation of individual gene expression at the transcriptional level is limited. Although transcription of most protein-coding mitochondrial genes occurs with the same frequency, steady-state levels of mature transcripts are different. Therefore, post-transcriptional processes are important for regulating mt-mRNA levels. The mitochondrial degradosome is a complex composed of the RNA helicase SUV3 (also known as SUPV3L1) and polynucleotide phosphorylase (PNPase, PNPT1). It is the best-characterized RNA-degrading machinery in human mitochondria, which is primarily responsible for the decay of mitochondrial antisense RNA. The mechanism of mitochondrial sense RNA decay is less understood. This review aims to provide a general picture of mitochondrial genome expression, with a particular focus on mitochondrial RNA (mtRNA) degradation.
Collapse
Affiliation(s)
- Giulia Santonoceto
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, Warsaw 02-106, Poland
| | - Aneta Jurkiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, Warsaw 02-106, Poland
| | - Roman J Szczesny
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, Warsaw 02-106, Poland
| |
Collapse
|
30
|
Vučković A, Freyer C, Wredenberg A, Hillen HS. The molecular machinery for maturation of primary mtDNA transcripts. Hum Mol Genet 2024; 33:R19-R25. [PMID: 38779769 PMCID: PMC11112384 DOI: 10.1093/hmg/ddae023] [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: 01/31/2024] [Revised: 01/31/2024] [Accepted: 02/08/2024] [Indexed: 05/25/2024] Open
Abstract
Human mitochondria harbour a circular, polyploid genome (mtDNA) encoding 11 messenger RNAs (mRNAs), two ribosomal RNAs (rRNAs) and 22 transfer RNAs (tRNAs). Mitochondrial transcription produces long, polycistronic transcripts that span almost the entire length of the genome, and hence contain all three types of RNAs. The primary transcripts then undergo a number of processing and maturation steps, which constitute key regulatory points of mitochondrial gene expression. The first step of mitochondrial RNA processing consists of the separation of primary transcripts into individual, functional RNA molecules and can occur by two distinct pathways. Both are carried out by dedicated molecular machineries that substantially differ from RNA processing enzymes found elsewhere. As a result, the underlying molecular mechanisms remain poorly understood. Over the last years, genetic, biochemical and structural studies have identified key players involved in both RNA processing pathways and provided the first insights into the underlying mechanisms. Here, we review our current understanding of RNA processing in mammalian mitochondria and provide an outlook on open questions in the field.
Collapse
MESH Headings
- Humans
- DNA, Mitochondrial/genetics
- RNA Processing, Post-Transcriptional
- Mitochondria/genetics
- Mitochondria/metabolism
- RNA, Mitochondrial/genetics
- RNA, Mitochondrial/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Animals
- Transcription, Genetic
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
Collapse
Affiliation(s)
- Ana Vučković
- Department of Cellular Biochemistry, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
- Research Group Structure and Function of Molecular Machines, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Christoph Freyer
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavägen 9, 171 65 Solna, Sweden
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Anna Steckséns gata 47, 171 64 Solna, Sweden
| | - Anna Wredenberg
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavägen 9, 171 65 Solna, Sweden
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Anna Steckséns gata 47, 171 64 Solna, Sweden
| | - Hauke S Hillen
- Department of Cellular Biochemistry, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
- Research Group Structure and Function of Molecular Machines, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), University of Göttingen, Robert-Koch-Straße 40, 37073 Göttingen, Germany
- Research Group Structure and Function of Molecular Machines, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Justus-von-Liebig-Weg 11, Goettingen 37077, Germany
| |
Collapse
|
31
|
Tang GX, Li ML, Zhou C, Huang ZS, Chen SB, Chen XC, Tan JH. Mitochondrial RelA empowers mtDNA G-quadruplex formation for hypoxia adaptation in cancer cells. Cell Chem Biol 2024:S2451-9456(24)00181-8. [PMID: 38821064 DOI: 10.1016/j.chembiol.2024.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 03/04/2024] [Accepted: 05/07/2024] [Indexed: 06/02/2024]
Abstract
Mitochondrial DNA (mtDNA) G-quadruplexes (G4s) have important regulatory roles in energy metabolism, yet their specific functions and underlying regulatory mechanisms have not been delineated. Using a chemical-genetic screening strategy, we demonstrated that the JAK/STAT3 pathway is the primary regulatory mechanism governing mtDNA G4 dynamics in hypoxic cancer cells. Further proteomic analysis showed that activation of the JAK/STAT3 pathway facilitates the translocation of RelA, a member of the NF-κB family, to the mitochondria, where RelA binds to mtDNA G4s and promotes their folding, resulting in increased mtDNA instability, inhibited mtDNA transcription, and subsequent mitochondrial dysfunction. This binding event disrupts the equilibrium of energy metabolism, catalyzing a metabolic shift favoring glycolysis. Collectively, the results provide insights into a strategy employed by cancer cells to adapt to hypoxia through metabolic reprogramming.
Collapse
Affiliation(s)
- Gui-Xue Tang
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Mao-Lin Li
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Cui Zhou
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zhi-Shu Huang
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, China; Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shuo-Bin Chen
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xiu-Cai Chen
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, China.
| | - Jia-Heng Tan
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, China; Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China.
| |
Collapse
|
32
|
Jafir M, Zhou L, Chen Y, Wan X. The first mitogenomic phylogenetic framework of Dorcus sensu lato (Coleoptera: Lucanidae), with an emphasis on generic taxonomy in Eastern Asia. BMC Ecol Evol 2024; 24:66. [PMID: 38773381 PMCID: PMC11107052 DOI: 10.1186/s12862-024-02225-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 03/14/2024] [Indexed: 05/23/2024] Open
Abstract
BACKGROUND Dorcus stag beetles in broad sense are one of the most diverse group in Lucanidae and important saproxylic insects playing a crucial role in nutrient recycling and forest biomonitoring. However, the dazzling morphological differentiations have caused numerous systematic confusion within the big genus, especially the puzzlingly generic taxonomy. So far, there is lack of molecular phylogenetic study to address the chaotic situation. In this study, we undertook mitochondrial genome sequencing of 42 representative species including 18 newly-sequenced ones from Eastern Asia and reconstructed the phylogenetic framework of stag beetles in Dorcus sensu lato for the first time. RESULTS The mitogenome datasets of Dorcus species have indicated the variable mitogenomic lengths ranged from 15,785 to 19,813 bp. Each mitogenome contained 13 PCGs, 2 rRNAs, 22 tRNAs, and a control region, and all PCGs were under strong purifying selection (Ka/Ks < 1). Notably, we have identified the presence of a substantial intergenic spacer (IGS) between the trnAser (UCN) and NAD1 genes, with varying lengths ranging from 129 bp (in D. hansi) to 158 bp (in D. tityus). The mitogenomic phylogenetic analysis of 42 species showed that Eastern Asia Dorcus was monophyletic, and divided into eight clades with significant genetic distance. Four of them, Clade VIII, VII, VI and I are clustered by the representative species of Serrognathus Motschulsky, Kirchnerius Schenk, Falcicornis Séguy and Dorcus s.s. respectively, which supported their fully generic positions as the previous morphological study presented. The topology also showed the remaining clades were distinctly separated from the species of Dorcus sensu lato, which implied that each of them might demonstrate independent generic status. The Linnaeus nomenclatures were suggested as Eurydorcus Didier stat. res., Eurytrachellelus Didier stat. res., Hemisodorcus Thomson stat. res. and Velutinodorcus Maes stat. res. For Clade V, IV, III and II respectively. CONCLUSION This study recognized the monophyly of Dorcus stag beetles and provided a framework for the molecular phylogeny of this group for the first time. The newly generated mitogenomic data serves as a valuable resource for future investigations on lucanid beetles. The generic relationship would facilitate the systematics of Dorcus stag beetles and thus be useful for exploring their evolutionary, ecological, and conservation aspects.
Collapse
Affiliation(s)
- Muhammad Jafir
- Department of Ecology, School of Resources and Environmental Engineering, Anhui University, 230601, Hefei, Anhui, China
| | - Liyang Zhou
- Department of Ecology, School of Resources and Environmental Engineering, Anhui University, 230601, Hefei, Anhui, China
| | - Yongjing Chen
- Department of Ecology, School of Resources and Environmental Engineering, Anhui University, 230601, Hefei, Anhui, China
| | - Xia Wan
- Department of Ecology, School of Resources and Environmental Engineering, Anhui University, 230601, Hefei, Anhui, China.
| |
Collapse
|
33
|
Mo R, Zhu D, Sun J, Yuan Q, Guo F, Duan Y. Molecular identification and phylogenetic analysis of the mitogenome in endangered giant nuthatch Sitta magna ( Passeriformes, Sittidae). Heliyon 2024; 10:e30513. [PMID: 38765151 PMCID: PMC11098796 DOI: 10.1016/j.heliyon.2024.e30513] [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: 04/20/2024] [Accepted: 04/29/2024] [Indexed: 05/21/2024] Open
Abstract
The Giant Nuthatch Sitta magna (family Sittidae) is a passerine bird, the quantification of the number of habitats and species on a global scale remains low. Most species are restricted to low elevations in southwest China, eastern Myanmar, and northern Thailand. To characterize the mitochondrial genome sequence of S. magna and its phylogenetic relationships with other members within the genus Sitta, the mitochondrial genome of S. magna was sequenced using the whole genome shotgun method. The sequencing results showed that the mitochondrial genome was 16,829 bp long and consisted of 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and one control region (D-loop). All tRNAs were predicted to form a typical clover secondary structure. Among the 13 PCGs, only the start codon in COI was ATC, the start codon by the remaining 12 PCGs was ATG, and the stop codons were TAG, TAA, AGG, AGA, and TA. Bayesian inference and maximum likelihood phylogenetic analysis of the sequences of 17 species generated consistent well-supported phylogenies. The family Polioptilidae and the family Troglodytidae were closely related, and the family Sittidae was confined to a single branch. The genus Sitta in the family Sittidae was mainly clustered into three branches. Our findings provide new mitochondrial genomic data that could be used for phylogenetic and taxonomic studies; our results also certificate into the phylogenetic relationships within the genus Sitta ((S. himalayensi+(S. nagaensis + S. europaea))+(S. villosa + S. yunnanensis))+(S. carolinensis + S. magna).
Collapse
Affiliation(s)
- Ruixin Mo
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Southwest Forestry University, Kunming, 650224, China
- College of Forestry, Southwest Forestry University, Kunming, Yunnan, 650224, China
| | - Dong Zhu
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Southwest Forestry University, Kunming, 650224, China
- College of Forestry, Southwest Forestry University, Kunming, Yunnan, 650224, China
| | - Jing Sun
- College of Forestry, Southwest Forestry University, Kunming, Yunnan, 650224, China
| | - Qingmiao Yuan
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Southwest Forestry University, Kunming, 650224, China
- College of Forestry, Southwest Forestry University, Kunming, Yunnan, 650224, China
| | - Feng Guo
- Administration of Zixi Mountain Provincial Nature Reserve, Chuxiong, 675008, China
| | - Yubao Duan
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Southwest Forestry University, Kunming, 650224, China
- College of Forestry, Southwest Forestry University, Kunming, Yunnan, 650224, China
| |
Collapse
|
34
|
Wang X, Zhao W, Cui S, Su B, Huang Y, Chen H. Characterization of the Mitogenome of the Genus Dendrocerus Ratzeburg (Hymenoptera: Megaspilidae) with the Specific Designed Primers. Animals (Basel) 2024; 14:1454. [PMID: 38791671 PMCID: PMC11117285 DOI: 10.3390/ani14101454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 05/05/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
In Hymenoptera, the monophyly of Evaniomorpha has been the focus of debate among different scholars. In this study, we sequenced two mitochondrial genomes of Dendrocerus (Hymenoptera: Megaspilidae) to analyze the mitochondrial genomic features of Dendrocerus and provide new molecular data for phylogenetic studies of Evaniomorpha. The mitogenome sizes of D. bellus and D. anisodontus were 15,445 bp and 15,373 bp, respectively, with the trnG of D. bellus missing. The nucleotide composition was significantly biased toward adenine and thymine, with A + T contents of 81.2% (D. bellus) and 82.4% (D. anisodontus). Using Ceraphron sp. (Ceraphronidae) as reference, the Ka/Ks values of NAD4L and NAD6 in D. anisodontus were both greater than one, indicating that non-synonymous mutations are favored by Darwinian selection, which is rare in other hymenopteran species. Compared with Ceraphon sp. gene order, nine operations were identified in D. anisodontus, including four reversals, four TDRLs (tandem duplication random losses) and one transposition, or four reversals and five TDRLs. Phylogenetic analysis of 40 mitochondrial genomes showed that Evaniomorpha was not a monophyletic group, which was also supported by the PBD values. Ceraphronoidea is a monophyletic group and is a sister to Aulacidae + Gasteruptiidae. Based on the conserved region of the newly sequenced mitochondrial genomes, a pair of specific primers MegaF/MegaR was designed for sequencing the COX1 genes in Megaspilidae and a 60% rate of success was achieved in the genus Dendrocerus.
Collapse
Affiliation(s)
- Xu Wang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (X.W.); (W.Z.); (S.C.)
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100000, China;
| | - Wenjing Zhao
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (X.W.); (W.Z.); (S.C.)
| | - Shanshan Cui
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (X.W.); (W.Z.); (S.C.)
| | - Baoshan Su
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-Founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu 241000, China;
| | - Yixin Huang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100000, China;
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-Founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu 241000, China;
| | - Huayan Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Chinese Academy of Sciences, Guangzhou 510650, China
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
| |
Collapse
|
35
|
Shi Q, Xie J, Wu J, Chen S, Sun G, Zhang J. Characterization of the complete mitochondrial genome of an endemic species in China, Aulocera merlina (Lepidoptera: Nymphalidae: Satyrinae) and phylogenetic analysis within Satyrinae. Ecol Evol 2024; 14:e11355. [PMID: 38694754 PMCID: PMC11061544 DOI: 10.1002/ece3.11355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 04/01/2024] [Accepted: 04/12/2024] [Indexed: 05/04/2024] Open
Abstract
The mitochondrial genome (mitogenome) has been extensively used as molecular markers in determining the insect phylogenetic relationships. In order to resolve the relationships among tribes and subtribes of Satyrinae at the mitochondrial genomic level, we obtained the complete mitogenome of Aulocera merlina (Oberthür, 1890) (Lepidoptera: Nymphalidae: Satyrinae) with a size of 15,259 bp. The mitogenome consisted of 37 typical genes, including 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and an A + T-rich region. The gene organization and arrangement were similar to those of all other known Satyrinae mitogenomes. All PCGs were initiated with the canonical codon pattern ATN, except for the cox1 gene, which used an atypical CGA codon. Nine PCGs used the complete stop codon TAA, while the remaining PCGs (cox1, cox2, nad4, and nad5) were terminated with a single T nucleotide. The canonical cloverleaf secondary structures were found in all tRNAs, except for trnS1 which lacked a dihydrouridine arm. The 448 bp A + T-rich region was located between rrnS and trnM, and it included the motif ATAGA followed by a 19-bp poly-T stretch and a microsatellite-like (TA)6 element preceded by the ATTTA motif. The phylogenetic tree, inferred using Bayesian inference and maximum likelihood methods, generated similar tree topologies, revealing well-supported monophyletic groups at the tribe level and recovering the relationship ((Satyrini + Melanitini) + ((Amathusiini + Elymniini) + Zetherini)). The close relationship between Satyrina and Melanargiina within the Satyrini was widely accepted. Additionally, Lethina, Parargina, and Mycalesina were closely related and collectively formed a sister group to Coenonymphina. Moreover, A. merlina was closely related to Oeneis buddha within the Satyrina. These findings will provide valuable information for future studies aiming to elucidate the phylogenetic relationships of Satyrinae.
Collapse
Affiliation(s)
- Qinghui Shi
- Fujian Provincial Key Laboratory of Resources and Environment Monitoring & Sustainable Management and UtilizationSanming UniversitySanmingChina
| | - Jinling Xie
- Fujian Provincial Key Laboratory of Resources and Environment Monitoring & Sustainable Management and UtilizationSanming UniversitySanmingChina
| | - Jialing Wu
- Fujian Provincial Key Laboratory of Resources and Environment Monitoring & Sustainable Management and UtilizationSanming UniversitySanmingChina
| | - Shengchung Chen
- Fujian Provincial Key Laboratory of Resources and Environment Monitoring & Sustainable Management and UtilizationSanming UniversitySanmingChina
| | - Gang Sun
- Fujian Provincial Key Laboratory of Resources and Environment Monitoring & Sustainable Management and UtilizationSanming UniversitySanmingChina
| | - Juncheng Zhang
- Fujian Provincial Key Laboratory of Resources and Environment Monitoring & Sustainable Management and UtilizationSanming UniversitySanmingChina
- Medical Plant Exploitation and Utilization Engineering Research CenterSanming UniversitySanmingChina
| |
Collapse
|
36
|
Singh J, Singh S, Emam EAF, Varshney U. Role of Rmd9p in 3'-end processing of mitochondrial 15S rRNA in Saccharomyces cerevisiae. Mitochondrion 2024; 76:101876. [PMID: 38599301 DOI: 10.1016/j.mito.2024.101876] [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: 12/15/2023] [Revised: 02/05/2024] [Accepted: 04/07/2024] [Indexed: 04/12/2024]
Abstract
Ribosome biogenesis, involving processing/assembly of rRNAs and r-proteins is a vital process. In Saccharomyces cerevisiae mitochondria, ribosomal small subunit comprises 15S rRNA (15S). While the 15S 5'-end processing uses Ccm1p and Pet127p, the mechanisms of the 3'-end processing remain unclear. We reveal involvement of Rmd9p in safeguarding/processing 15S 3'-end. Rmd9p deficiency results in a cleavage at a position 183 nucleotides upstream of 15S 3'-end, and in the loss of the 3'-minor domain. Rmd9p binds to the sequences in the 3'-end region of 15S, and a genetic interaction between rmd9 and dss1 indicates that Rmd9p regulates/limits mtEXO activity during the 3'-end spacer processing.
Collapse
Affiliation(s)
- Jitendra Singh
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Sudhir Singh
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Elhassan Ali Fathi Emam
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India; Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India.
| |
Collapse
|
37
|
Zhang D, Chen X, Yang J, Yi W, Xie Q, Yang H, Sweet MH, Bu W, Li T. Phylogenetic placement and comparative analysis of the mitochondrial genomes of Idiostoloidea (Hemiptera: Heteroptera). Ecol Evol 2024; 14:e11328. [PMID: 38698924 PMCID: PMC11063732 DOI: 10.1002/ece3.11328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 04/06/2024] [Accepted: 04/10/2024] [Indexed: 05/05/2024] Open
Abstract
The classification system and the higher level phylogenetic relationships of Pentatomomorpha, the second largest infraorder of Heteroptera (Insecta: Hemiptera), have been debated and remain controversial over decades. In particular, the placement and phylogenetic relationship of Idiostoloidea are not well resolved, which hampers a better understanding of the evolutionary history of Pentatomomorpha. In this study, for the first time, we reported the complete mitochondrial genome for two narrowly distributed families of Idiostoloidea (including Idiostolidae and Henicocoridae), respectively. The length of the mitochondrial genome of Monteithocoris hirsutus and Henicocoris sp. is 16,632 and 16,013 bp, respectively. The content of AT is ranging from 75.15% to 80.48%. The mitogenomic structure of Idiostoloidea is highly conservative and there are no gene arrangements. By using the Bayesian inference, maximum likelihood, and Bayesian site-heterogeneous mixture model, we inferred the phylogenetic relationships within Pentatomomorpha and estimated their divergence times based on concatenated mitogenomes and nuclear ribosomal genes. Our results support the classification system of six superfamilies within Pentatomomorpha and confirm the monophyletic groups of each superfamily, with the following phylogenetic relationships: (Aradoidea + (Pentatomoidea + (Idiostoloidea + (Coreoidea + (Pyrrhocoroidea + Lygaeoidea))))). Furthermore, estimated divergence times revealed that most pentatomomorphan superfamilies and families diverged during the Late Jurassic to Early Cretaceous, which coincides with the explosive radiation of angiosperms.
Collapse
Affiliation(s)
- Danli Zhang
- College of Biological Sciences and TechnologyTaiyuan Normal UniversityJinzhongChina
| | - XiaoYan Chen
- College of Biological Sciences and TechnologyTaiyuan Normal UniversityJinzhongChina
| | - Jingjing Yang
- College of Biological Sciences and TechnologyTaiyuan Normal UniversityJinzhongChina
| | - Wenbo Yi
- Institute of Entomology, College of Life SciencesNankai UniversityTianjinChina
| | - Qiang Xie
- Institute of Entomology, College of Life SciencesNankai UniversityTianjinChina
| | - HuanHuan Yang
- School of BioengineeringQilu University of Technology (Shandong Academy of Sciences)JinanChina
| | - Merrill H. Sweet
- Department of Entomology, Plant Pathology, and Weed ScienceNew Mexico State UniversityLas CrucesNew MexicoUSA
| | - Wenjun Bu
- Institute of Entomology, College of Life SciencesNankai UniversityTianjinChina
| | - Teng Li
- Institute of Entomology, College of Life SciencesNankai UniversityTianjinChina
- School of Biological SciencesUniversity of AucklandAucklandNew Zealand
| |
Collapse
|
38
|
Liao X, Shih Y, Jia C, Gao T. Complete Mitochondrial Genome of Four Peristediidae Fish Species: Genome Characterization and Phylogenetic Analysis. Genes (Basel) 2024; 15:557. [PMID: 38790187 PMCID: PMC11121196 DOI: 10.3390/genes15050557] [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: 03/23/2024] [Revised: 04/23/2024] [Accepted: 04/23/2024] [Indexed: 05/26/2024] Open
Abstract
The systematic revision of the family Peristediidae remains an unresolved issue due to their diverse and unique morphology. Despite the popularity of using mitochondrial genome research to comprehensively understand phylogenetic relationships in fish, genetic data for peristediid fish need to be included. Therefore, this study aims to investigate the mitochondrial genomic characteristics and intra-family phylogenetic relationships of Peristediidae by utilizing mitochondrial genome analysis. Therefore, this study aims to investigate the phylogenetic relationship of Peristediidae by utilizing mitochondrial genome analysis. The mitochondrial genome of four species of Peristediidae (Peristedion liorhynchus, Satyrichthys welchi, Satyrichthys rieffeli, and Scalicus amiscus) collected in the East China Sea was studied. The mitochondrial gene sequence lengths of four fish species were 16,533 bp, 16,526 bp, 16,527 bp, and 16,526 bp, respectively. They had the same mitochondrial structure and were all composed of 37 genes and one control region. Most PCGs used ATG as the start codon, and a few used GTG as the start codon. An incomplete stop codon (TA/T) occurred. The AT-skew and GC-skew values of 13 PCGs from four species were negative, and the GC-skew amplitude was greater than that of AT-skew. All cases of D-arm were found in tRNA-Ser (GCT). The Ka/Ks ratio analysis indicated that 13 PCGs were suffering purifying selection. Based on 12 PCGs (excluding ND6) sequences, a phylogenetic tree was constructed using Bayesian inference (BI) and maximum likelihood (ML) methods, providing a further supplement to the scientific classification of Peristediidae fish. According to the results of divergence time, the four species of fish had apparent divergence in the Early Cenozoic, which indicates that the geological events at that time caused the climax of species divergence and evolution.
Collapse
Affiliation(s)
- Xianhui Liao
- Fisheries College, Zhejiang Ocean University, Zhoushan 316022, China;
| | - Yijia Shih
- Fisheries College, Jimei University, Xiamen 361021, China;
| | - Chenghao Jia
- School of Ecology and Environment, Hainan University, Haikou 570228, China;
| | - Tianxiang Gao
- Fisheries College, Zhejiang Ocean University, Zhoushan 316022, China;
| |
Collapse
|
39
|
McShane E, Couvillion M, Ietswaart R, Prakash G, Smalec BM, Soto I, Baxter-Koenigs AR, Choquet K, Churchman LS. A kinetic dichotomy between mitochondrial and nuclear gene expression processes. Mol Cell 2024; 84:1541-1555.e11. [PMID: 38503286 PMCID: PMC11236289 DOI: 10.1016/j.molcel.2024.02.028] [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: 09/05/2023] [Revised: 12/12/2023] [Accepted: 02/27/2024] [Indexed: 03/21/2024]
Abstract
Oxidative phosphorylation (OXPHOS) complexes, encoded by both mitochondrial and nuclear DNA, are essential producers of cellular ATP, but how nuclear and mitochondrial gene expression steps are coordinated to achieve balanced OXPHOS subunit biogenesis remains unresolved. Here, we present a parallel quantitative analysis of the human nuclear and mitochondrial messenger RNA (mt-mRNA) life cycles, including transcript production, processing, ribosome association, and degradation. The kinetic rates of nearly every stage of gene expression differed starkly across compartments. Compared with nuclear mRNAs, mt-mRNAs were produced 1,100-fold more, degraded 7-fold faster, and accumulated to 160-fold higher levels. Quantitative modeling and depletion of mitochondrial factors LRPPRC and FASTKD5 identified critical points of mitochondrial regulatory control, revealing that the mitonuclear expression disparities intrinsically arise from the highly polycistronic nature of human mitochondrial pre-mRNA. We propose that resolving these differences requires a 100-fold slower mitochondrial translation rate, illuminating the mitoribosome as a nexus of mitonuclear co-regulation.
Collapse
Affiliation(s)
- Erik McShane
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Mary Couvillion
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Robert Ietswaart
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Gyan Prakash
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Brendan M Smalec
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Iliana Soto
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Autum R Baxter-Koenigs
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Karine Choquet
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - L Stirling Churchman
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
40
|
Wang Y, Chen S, Liu Y, Zhang S, Jin X, Zheng S, Li J, Peng Y, Zhang K, Zhang C, Liu B. Comparative Analysis of the Complete Mitochondrial Genomes of Three Sisoridae (Osteichthyes, Siluriformes) and the Phylogenetic Relationships of Sisoridae. Biochem Genet 2024:10.1007/s10528-024-10793-7. [PMID: 38635013 DOI: 10.1007/s10528-024-10793-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 03/21/2024] [Indexed: 04/19/2024]
Abstract
The family Sisoridae is one of the largest and most diverse Asiatic catfish families, with most species occurring in the water systems of the Qinhai-Tibetan Plateau and East Himalayas. At present, the phylogenetic relationship of the Sisoridae is relatively chaotic. In this study, the mitochondrial genomes (mitogenomes) of three species Creteuchiloglanis kamengensis, Glaridoglanis andersonii, and Exostoma sp. were systematically investigated, the phylogenetic relationships of the family were reconstructed and to determine the phylogenetic position of Exostoma sp. within Sisoridae. The lengths of the mitogenomes' sequences of C. kamengensis, G. andersonii, and Exostoma sp. were 16,589 bp, 16,531 bp, and 16,529 bp, respectively. They all contained one identical control region (D-loop), two ribosomal RNAs (rRNAs), 13 protein-coding genes (PCGs) and 22 transfer RNA (tRNA) genes. We applied two approaches, Bayesian Inference (BI) and Maximum Likelihood (ML), to construct phylogenetic trees. Our findings revealed that the topological structure of both ML and BI trees exhibited significant congruence. Specifically, the phylogenetic tree strongly supports the monophyly of Sisorinae and Glyptosternoids and provides new molecular biological data to support the reconstruction of phylogenetic relationships with Sisoridae. This study is of great scientific value for phylogenetic and genetic variation studies of the Sisoridae.
Collapse
Affiliation(s)
- Yunpeng Wang
- National engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No.1, Haida South Road, Zhoushan, 316022, Zhejiang, People's Republic of China
| | - Shiyi Chen
- National engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No.1, Haida South Road, Zhoushan, 316022, Zhejiang, People's Republic of China
| | - Yifan Liu
- National engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No.1, Haida South Road, Zhoushan, 316022, Zhejiang, People's Republic of China
| | - Shufei Zhang
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou, 510300, Guangdong, China
| | - Xun Jin
- National engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No.1, Haida South Road, Zhoushan, 316022, Zhejiang, People's Republic of China
| | - Sixu Zheng
- National engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No.1, Haida South Road, Zhoushan, 316022, Zhejiang, People's Republic of China
| | - Jiasheng Li
- National engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No.1, Haida South Road, Zhoushan, 316022, Zhejiang, People's Republic of China
| | - Ying Peng
- National engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No.1, Haida South Road, Zhoushan, 316022, Zhejiang, People's Republic of China
| | - Kun Zhang
- National engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No.1, Haida South Road, Zhoushan, 316022, Zhejiang, People's Republic of China
| | - Chi Zhang
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China.
| | - Bingjian Liu
- National engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No.1, Haida South Road, Zhoushan, 316022, Zhejiang, People's Republic of China.
| |
Collapse
|
41
|
Koster CC, Kleefeldt AA, van den Broek M, Luttik M, Daran JM, Daran-Lapujade P. Long-read direct RNA sequencing of the mitochondrial transcriptome of Saccharomyces cerevisiae reveals condition-dependent intron abundance. Yeast 2024; 41:256-278. [PMID: 37642136 DOI: 10.1002/yea.3893] [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: 05/31/2023] [Revised: 07/11/2023] [Accepted: 07/18/2023] [Indexed: 08/31/2023] Open
Abstract
Mitochondria fulfil many essential roles and have their own genome, which is expressed as polycistronic transcripts that undergo co- or posttranscriptional processing and splicing. Due to the inherent complexity and limited technical accessibility of the mitochondrial transcriptome, fundamental questions regarding mitochondrial gene expression and splicing remain unresolved, even in the model eukaryote Saccharomyces cerevisiae. Long-read sequencing could address these fundamental questions. Therefore, a method for the enrichment of mitochondrial RNA and sequencing using Nanopore technology was developed, enabling the resolution of splicing of polycistronic genes and the quantification of spliced RNA. This method successfully captured the full mitochondrial transcriptome and resolved RNA splicing patterns with single-base resolution and was applied to explore the transcriptome of S. cerevisiae grown with glucose or ethanol as the sole carbon source, revealing the impact of growth conditions on mitochondrial RNA expression and splicing. This study uncovered a remarkable difference in the turnover of Group II introns between yeast grown in either mostly fermentative or fully respiratory conditions. Whether this accumulation of introns in glucose medium has an impact on mitochondrial functions remains to be explored. Combined with the high tractability of the model yeast S. cerevisiae, the developed method enables to monitor mitochondrial transcriptome responses in a broad range of relevant contexts, including oxidative stress, apoptosis and mitochondrial diseases.
Collapse
Affiliation(s)
- Charlotte C Koster
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Askar A Kleefeldt
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Marcel van den Broek
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Marijke Luttik
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Jean-Marc Daran
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | | |
Collapse
|
42
|
Despabiladeras JB, Bautista MAM. Complete Mitochondrial Genome of the Eggplant Fruit and Shoot Borer, Leucinodes orbonalis Guenée (Lepidoptera: Crambidae), and Comparison with Other Pyraloid Moths. INSECTS 2024; 15:220. [PMID: 38667350 PMCID: PMC11050083 DOI: 10.3390/insects15040220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 03/17/2024] [Accepted: 03/18/2024] [Indexed: 04/28/2024]
Abstract
The eggplant fruit and shoot borer (EFSB) (Leucinodes orbonalis Guenée) is a devastating lepidopteran pest of eggplant (Solanum melongena L.) in the Philippines. Management of an insect pest like the EFSB requires an understanding of its biology, evolution, and adaptations. Genomic resources provide a starting point for understanding EFSB biology, as the resources can be used for phylogenetics and population structure studies. To date, genomic resources are scarce for EFSB; thus, this study generated its complete mitochondrial genome (mitogenome). The circular mitogenome is 15,244 bp-long. It contains 37 genes, namely 13 protein-coding, 22 tRNA, and 2 rRNA genes, and has conserved noncoding regions, motifs, and gene syntenies characteristic of lepidopteran mitogenomes. Some protein-coding genes start and end with non-canonical codons. The tRNA genes exhibit a conserved cloverleaf structure, with the exception in trnS1. Partitioned phylogenetic analysis using 72 pyraloids generated highly supported maximum likelihood and Bayesian inference trees revealing expected basal splits between Crambidae and Pyralidae, and Spilomelinae and Pyraustinae. Spilomelinae was recovered to be paraphyletic, with the EFSB robustly placed before the split of Spilomelinae and Pyraustinae. Overall, the EFSB mitogenome resource will be useful for delineations within Spilomelinae and population structure analysis.
Collapse
Affiliation(s)
| | - Ma. Anita M. Bautista
- Functional Genomics Laboratory, National Institute of Molecular Biology and Biotechnology, College of Science, University of the Philippines-Diliman, Quezon City 1101, Philippines;
| |
Collapse
|
43
|
Benito JB, Porter ML, Niemiller ML. Comparative mitogenomic analysis of subterranean and surface amphipods (Crustacea, Amphipoda) with special reference to the family Crangonyctidae. BMC Genomics 2024; 25:298. [PMID: 38509489 PMCID: PMC10956265 DOI: 10.1186/s12864-024-10111-w] [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: 06/20/2023] [Accepted: 02/09/2024] [Indexed: 03/22/2024] Open
Abstract
Mitochondrial genomes play important roles in studying genome evolution, phylogenetic analyses, and species identification. Amphipods (Class Malacostraca, Order Amphipoda) are one of the most ecologically diverse crustacean groups occurring in a diverse array of aquatic and terrestrial environments globally, from freshwater streams and lakes to groundwater aquifers and the deep sea, but we have a limited understanding of how habitat influences the molecular evolution of mitochondrial energy metabolism. Subterranean amphipods likely experience different evolutionary pressures on energy management compared to surface-dwelling taxa that generally encounter higher levels of predation and energy resources and live in more variable environments. In this study, we compared the mitogenomes, including the 13 protein-coding genes involved in the oxidative phosphorylation (OXPHOS) pathway, of surface and subterranean amphipods to uncover potentially different molecular signals of energy metabolism between surface and subterranean environments in this diverse crustacean group. We compared base composition, codon usage, gene order rearrangement, conducted comparative mitogenomic and phylogenomic analyses, and examined evolutionary signals of 35 amphipod mitogenomes representing 13 families, with an emphasis on Crangonyctidae. Mitogenome size, AT content, GC-skew, gene order, uncommon start codons, location of putative control region (CR), length of rrnL and intergenic spacers differed between surface and subterranean amphipods. Among crangonyctid amphipods, the spring-dwelling Crangonyx forbesi exhibited a unique gene order, a long nad5 locus, longer rrnL and rrnS loci, and unconventional start codons. Evidence of directional selection was detected in several protein-encoding genes of the OXPHOS pathway in the mitogenomes of surface amphipods, while a signal of purifying selection was more prominent in subterranean species, which is consistent with the hypothesis that the mitogenome of surface-adapted species has evolved in response to a more energy demanding environment compared to subterranean amphipods. Overall, gene order, locations of non-coding regions, and base-substitution rates points to habitat as an important factor influencing the evolution of amphipod mitogenomes.
Collapse
Affiliation(s)
- Joseph B Benito
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL, 35899, USA
| | - Megan L Porter
- School of Life Sciences, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Matthew L Niemiller
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL, 35899, USA.
| |
Collapse
|
44
|
Zhang G, Xu T, Chen Y, Xu W, Wang Y, Li Y, Zhu F, Liu H, Ruan H. Complete Mitochondrial Genomes of Nedyopus patrioticus: New Insights into the Color Polymorphism of Millipedes. Curr Issues Mol Biol 2024; 46:2514-2527. [PMID: 38534775 DOI: 10.3390/cimb46030159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 03/04/2024] [Accepted: 03/13/2024] [Indexed: 03/28/2024] Open
Abstract
There has been debate about whether individuals with different color phenotypes should have different taxonomic status. In order to determine whether the different color phenotypes of Nedyopus patrioticus require separate taxonomic status or are simply synonyms, here, the complete mitochondrial genomes (mitogenomes) of two different colored N. patrioticus, i.e., red N. patrioticus and white N. patrioticus, are presented. The two mitogenomes were 15,781 bp and 15,798 bp in length, respectively. Each mitogenome contained 13 PCGs, 19 tRNAs, 2 rRNAs, and 1 CR, with a lack of trnI, trnL2, and trnV compared to other Polydesmida species. All genes were located on a single strand in two mitogenomes. Mitochondrial DNA analyses revealed that red N. patrioticus and white N. patrioticus did not show clear evolutionary differences. Furthermore, no significant divergence was discovered by means of base composition analysis. As a result, we suggest that white N. patrioticus might be regarded as a synonym for red N. patrioticus. The current findings confirmed the existence of color polymorphism in N. patrioticus, which provides exciting possibilities for future research. It is necessary to apply a combination of molecular and morphological methods in the taxonomy of millipedes.
Collapse
Affiliation(s)
- Gaoji Zhang
- College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Tangjun Xu
- College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Yukun Chen
- College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Wei Xu
- College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Yinuo Wang
- College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Yuanyuan Li
- College of Ecology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Fuyuan Zhu
- College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Hongyi Liu
- College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
- College of Ecology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Honghua Ruan
- College of Ecology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| |
Collapse
|
45
|
Rossmanith W, Giegé P, Hartmann RK. Discovery, structure, mechanisms, and evolution of protein-only RNase P enzymes. J Biol Chem 2024; 300:105731. [PMID: 38336295 PMCID: PMC10941002 DOI: 10.1016/j.jbc.2024.105731] [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: 08/01/2023] [Revised: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 02/12/2024] Open
Abstract
The endoribonuclease RNase P is responsible for tRNA 5' maturation in all domains of life. A unique feature of RNase P is the variety of enzyme architectures, ranging from dual- to multi-subunit ribonucleoprotein forms with catalytic RNA subunits to protein-only enzymes, the latter occurring as single- or multi-subunit forms or homo-oligomeric assemblies. The protein-only enzymes evolved twice: a eukaryal protein-only RNase P termed PRORP and a bacterial/archaeal variant termed homolog of Aquifex RNase P (HARP); the latter replaced the RNA-based enzyme in a small group of thermophilic bacteria but otherwise coexists with the ribonucleoprotein enzyme in a few other bacteria as well as in those archaea that also encode a HARP. Here we summarize the history of the discovery of protein-only RNase P enzymes and review the state of knowledge on structure and function of bacterial HARPs and eukaryal PRORPs, including human mitochondrial RNase P as a paradigm of multi-subunit PRORPs. We also describe the phylogenetic distribution and evolution of PRORPs, as well as possible reasons for the spread of PRORPs in the eukaryal tree and for the recruitment of two additional protein subunits to metazoan mitochondrial PRORP. We outline potential applications of PRORPs in plant biotechnology and address diseases associated with mutations in human mitochondrial RNase P genes. Finally, we consider possible causes underlying the displacement of the ancient RNA enzyme by a protein-only enzyme in a small group of bacteria.
Collapse
Affiliation(s)
- Walter Rossmanith
- Center for Anatomy & Cell Biology, Medical University of Vienna, Vienna, Austria.
| | - Philippe Giegé
- Institute for Plant Molecular Biology, IBMP-CNRS, University of Strasbourg, Strasbourg, France.
| | - Roland K Hartmann
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany.
| |
Collapse
|
46
|
Wilhelm CA, Kaitany K, Kelly A, Yacoub M, Koutmos M. The protein-only RNase Ps, endonucleases that cleave pre-tRNA: Biological relevance, molecular architectures, substrate recognition and specificity, and protein interactomes. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1836. [PMID: 38453211 DOI: 10.1002/wrna.1836] [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: 11/15/2023] [Revised: 01/27/2024] [Accepted: 02/06/2024] [Indexed: 03/09/2024]
Abstract
Protein-only RNase P (PRORP) is an essential enzyme responsible for the 5' maturation of precursor tRNAs (pre-tRNAs). PRORPs are classified into three categories with unique molecular architectures, although all three classes of PRORPs share a mechanism and have similar active sites. Single subunit PRORPs, like those found in plants, have multiple isoforms with different localizations, substrate specificities, and temperature sensitivities. Most recently, Arabidopsis thaliana PRORP2 was shown to interact with TRM1A and B, highlighting a new potential role between these enzymes. Work with At PRORPs led to the development of a ribonuclease that is being used to protect against plant viruses. The mitochondrial RNase P complex, found in metazoans, consists of PRORP, TRMT10C, and SDR5C1, and has also been shown to have substrate specificity, although the cause is unknown. Mutations in mitochondrial tRNA and mitochondrial RNase P have been linked to human disease, highlighting the need to continue understanding this complex. The last class of PRORPs, homologs of Aquifex RNase P (HARPs), is found in thermophilic archaea and bacteria. This most recently discovered type of PRORP forms a large homo-oligomer complex. Although numerous structures of HARPs have been published, it is still unclear how HARPs bind pre-tRNAs and in what ratio. There is also little investigation into the substrate specificity and ideal conditions for HARPs. Moving forward, further work is required to fully characterize each of the three classes of PRORP, the pre-tRNA binding recognition mechanism, the rules of substrate specificity, and how these three distinct classes of PRORP evolved. This article is categorized under: RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems.
Collapse
Affiliation(s)
| | - Kipchumba Kaitany
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
- Program in Biophysics, University of Michigan, Ann Arbor, Michigan, USA
| | - Abigail Kelly
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Matthew Yacoub
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Markos Koutmos
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
- Program in Biophysics, University of Michigan, Ann Arbor, Michigan, USA
| |
Collapse
|
47
|
Pennance T, Calvelo J, Tennessen JA, Burd R, Cayton J, Bollmann SR, Blouin MS, Spaan JM, Hoffmann FG, Ogara G, Rawago F, Andiego K, Mulonga B, Odhiambo M, Loker ES, Laidemitt MR, Lu L, Iriarte A, Odiere MR, Steinauer ML. The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni. BMC Genomics 2024; 25:192. [PMID: 38373909 PMCID: PMC10875847 DOI: 10.1186/s12864-024-10103-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 02/08/2024] [Indexed: 02/21/2024] Open
Abstract
BACKGROUND Control and elimination of schistosomiasis is an arduous task, with current strategies proving inadequate to break transmission. Exploration of genetic approaches to interrupt Schistosoma mansoni transmission, the causative agent for human intestinal schistosomiasis in sub-Saharan Africa and South America, has led to genomic research of the snail vector hosts of the genus Biomphalaria. Few complete genomic resources exist, with African Biomphalaria species being particularly underrepresented despite this being where the majority of S. mansoni infections occur. Here we generate and annotate the first genome assembly of Biomphalaria sudanica sensu lato, a species responsible for S. mansoni transmission in lake and marsh habitats of the African Rift Valley. Supported by whole-genome diversity data among five inbred lines, we describe orthologs of immune-relevant gene regions in the South American vector B. glabrata and present a bioinformatic pipeline to identify candidate novel pathogen recognition receptors (PRRs). RESULTS De novo genome and transcriptome assembly of inbred B. sudanica originating from the shoreline of Lake Victoria (Kisumu, Kenya) resulted in a haploid genome size of ~ 944.2 Mb (6,728 fragments, N50 = 1.067 Mb), comprising 23,598 genes (BUSCO = 93.6% complete). The B. sudanica genome contains orthologues to all described immune genes/regions tied to protection against S. mansoni in B. glabrata, including the polymorphic transmembrane clusters (PTC1 and PTC2), RADres, and other loci. The B. sudanica PTC2 candidate immune genomic region contained many PRR-like genes across a much wider genomic region than has been shown in B. glabrata, as well as a large inversion between species. High levels of intra-species nucleotide diversity were seen in PTC2, as well as in regions linked to PTC1 and RADres orthologues. Immune related and putative PRR gene families were significantly over-represented in the sub-set of B. sudanica genes determined as hyperdiverse, including high extracellular diversity in transmembrane genes, which could be under pathogen-mediated balancing selection. However, no overall expansion in immunity related genes was seen in African compared to South American lineages. CONCLUSIONS The B. sudanica genome and analyses presented here will facilitate future research in vector immune defense mechanisms against pathogens. This genomic/transcriptomic resource provides necessary data for the future development of molecular snail vector control/surveillance tools, facilitating schistosome transmission interruption mechanisms in Africa.
Collapse
Affiliation(s)
- Tom Pennance
- College of Osteopathic Medicine of the Pacific - Northwest, Western University of Health Sciences, Lebanon, OR, USA.
| | - Javier Calvelo
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Facultad de Medicina, Instituto de Higiene, Universidad de La República, Montevideo, 11600, Uruguay
| | | | - Ryan Burd
- College of Osteopathic Medicine of the Pacific - Northwest, Western University of Health Sciences, Lebanon, OR, USA
| | - Jared Cayton
- College of Osteopathic Medicine of the Pacific - Northwest, Western University of Health Sciences, Lebanon, OR, USA
| | | | | | - Johannie M Spaan
- College of Osteopathic Medicine of the Pacific - Northwest, Western University of Health Sciences, Lebanon, OR, USA
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Starkville, MS, USA
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS, USA
| | - George Ogara
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), P. O. Box 1578-40100, Kisumu, Kenya
| | - Fredrick Rawago
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), P. O. Box 1578-40100, Kisumu, Kenya
| | - Kennedy Andiego
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), P. O. Box 1578-40100, Kisumu, Kenya
| | - Boaz Mulonga
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), P. O. Box 1578-40100, Kisumu, Kenya
| | - Meredith Odhiambo
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), P. O. Box 1578-40100, Kisumu, Kenya
| | - Eric S Loker
- Center for Evolutionary and Theoretical Immunology, Parasite Division Museum of Southwestern Biology, Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | - Martina R Laidemitt
- Center for Evolutionary and Theoretical Immunology, Parasite Division Museum of Southwestern Biology, Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | - Lijun Lu
- Center for Evolutionary and Theoretical Immunology, Parasite Division Museum of Southwestern Biology, Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | - Andrés Iriarte
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Facultad de Medicina, Instituto de Higiene, Universidad de La República, Montevideo, 11600, Uruguay
| | - Maurice R Odiere
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), P. O. Box 1578-40100, Kisumu, Kenya
| | - Michelle L Steinauer
- College of Osteopathic Medicine of the Pacific - Northwest, Western University of Health Sciences, Lebanon, OR, USA.
| |
Collapse
|
48
|
Zhang G, Gao M, Chen Y, Wang Y, Gan T, Zhu F, Liu H. The First Complete Mitochondrial Genome of the Genus Litostrophus: Insights into the Rearrangement and Evolution of Mitochondrial Genomes in Diplopoda. Genes (Basel) 2024; 15:254. [PMID: 38397243 PMCID: PMC10888367 DOI: 10.3390/genes15020254] [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: 01/02/2024] [Revised: 02/13/2024] [Accepted: 02/17/2024] [Indexed: 02/25/2024] Open
Abstract
This study presents the complete mitochondrial genome (mitogenome) of Litostrophus scaber, which is the first mitogenome of the genus Litostrophus. The mitogenome is a circular molecule with a length of 15,081 bp. The proportion of adenine and thymine (A + T) was 69.25%. The gene ND4L used TGA as the initiation codon, while the other PCGs utilized ATN (A, T, G, C) as the initiation codons. More than half of the PCGs used T as an incomplete termination codon. The transcription direction of the L. scaber mitogenome matched Spirobolus bungii, in contrast to most millipedes. Novel rearrangements were found in the L. scaber mitogenome: trnQ -trnC and trnL1- trnP underwent short-distance translocations and the gene block rrnS-rrnL-ND1 moved to a position between ND4 and ND5, resulting in the formation of a novel gene order. The phylogenetic analysis showed that L. scaber is most closely related to S. bungii, followed by Narceus magnum. These findings enhance our understanding of the rearrangement and evolution of Diplopoda mitogenomes.
Collapse
Affiliation(s)
- Gaoji Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (G.Z.); (M.G.); (Y.C.); (Y.W.); (F.Z.)
| | - Ming Gao
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (G.Z.); (M.G.); (Y.C.); (Y.W.); (F.Z.)
| | - Yukun Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (G.Z.); (M.G.); (Y.C.); (Y.W.); (F.Z.)
| | - Yinuo Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (G.Z.); (M.G.); (Y.C.); (Y.W.); (F.Z.)
| | - Tianyi Gan
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao 266109, China;
| | - Fuyuan Zhu
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (G.Z.); (M.G.); (Y.C.); (Y.W.); (F.Z.)
| | - Hongyi Liu
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (G.Z.); (M.G.); (Y.C.); (Y.W.); (F.Z.)
| |
Collapse
|
49
|
Zheng C, Zhu X, Wang Y, Dong X, Yang R, Tang Z, Bu W. Mitogenomes Provide Insights into the Species Boundaries and Phylogenetic Relationships among Three Dolycoris Sloe Bugs (Hemiptera: Pentatomidae) from China. INSECTS 2024; 15:134. [PMID: 38392553 PMCID: PMC10889809 DOI: 10.3390/insects15020134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 02/24/2024]
Abstract
(1) Background: The three sloe bugs, Dolycoris baccarum, Dolycoris indicus, and Dolycoris penicillatus, are found in the Chinese mainland and are morphologically similar. The species boundaries and phylogenetic relationships of the three species remain uncertain; (2) Methods: In this study, we generated multiple mitochondrial genomes (mitogenomes) for each of the three species and conducted comparative mitogenomic analysis, species delimitation, and phylogenetic analysis based on these data; (3) Results: Mitogenomes of the three Dolycoris species are conserved in nucleotide composition, gene arrangement, and codon usage. All protein-coding genes (PCGs) were found to be under purifying selection, and the ND4 evolved at the fastest rate. Most species delimitation analyses based on the COI gene and the concatenated 13 PCGs retrieved three operational taxonomic units (OTUs), which corresponded well with the three Dolycoris species identified based on morphological characters. A clear-cut barcode gap was discovered between the interspecific and intraspecific genetic distances of the three Dolycoris species. Phylogenetic analyses strongly supported the monophyly of Dolycoris, with interspecific relationship inferred as (D. indicus + (D. baccarum + D. penicillatus)); (4) Conclusions: Our study provides the first insight into the species boundaries and phylogenetic relationships of the three Dolycoris species distributed across the Chinese mainland.
Collapse
Affiliation(s)
- Chenguang Zheng
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Xiuxiu Zhu
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Ying Wang
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Xue Dong
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Ruijuan Yang
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Zechen Tang
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| |
Collapse
|
50
|
Tao K, Gao Y, Yin H, Liang Q, Yang Q, Yu X. Comparative Mitogenome Analyses of Fifteen Ramshorn Snails and Insights into the Phylogeny of Planorbidae (Gastropoda: Hygrophila). Int J Mol Sci 2024; 25:2279. [PMID: 38396956 PMCID: PMC10889216 DOI: 10.3390/ijms25042279] [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: 01/09/2024] [Revised: 02/08/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
Ramshorn snails from the family Planorbidae are important freshwater snails due to their low trophic level, and some of them act as intermediate hosts for zoonotic trematodes. There are about 250 species from 40 genera of Planorbidae, but only 14 species from 5 genera (Anisus, Biomphalaria, Bulinus, Gyraulus, and Planorbella) have sequenced complete mitochondrial genomes (mitogenomes). In this study, we sequenced and assembled a high-quality mitogenome of a ramshorn snail, Polypylis sp. TS-2018, which represented the first mitogenome of the genus. The mitogenome of Polypylis sp. TS-2018 is 13,749 bp in length, which is shorter than that of most gastropods. It contains 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and 2 ribosomal RNA (rRNA). We compared mitogenome characteristics, selection pressure, and gene rearrangement among all of the available mitogenomes of ramshorn snails. We found that the nonsynonymous and synonymous substitution rates (Ka/Ks) of most PCGs indicated purifying and negative selection, except for atp8 of Anisus, Biomphalaria, and Gyraulus, which indicated positive selection. We observed that transpositions and reverse transpositions occurred on 10 tRNAs and rrnS, which resulted in six gene arrangement types. We reconstructed the phylogenetic trees using the sequences of PCGs and rRNAs and strongly supported the monophyly of each genus, as well as three tribes in Planorbidae. Both the gene rearrangement and phylogenetic results suggested that Polypylis had a close relationship with Anisus and Gyraulus, while Bulinus was the sister group to all of the other genera. Our results provide useful data for further investigation of species identification, population genetics, and phylogenetics among ramshorn snails.
Collapse
Affiliation(s)
| | | | | | | | - Qianqian Yang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou 310018, China; (K.T.); (Y.G.); (H.Y.); (Q.L.)
| | - Xiaoping Yu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou 310018, China; (K.T.); (Y.G.); (H.Y.); (Q.L.)
| |
Collapse
|