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Hao J, Liang Y, Ping J, Li J, Shi W, Su Y, Wang T. Chloroplast gene expression level is negatively correlated with evolutionary rates and selective pressure while positively with codon usage bias in Ophioglossum vulgatum L. BMC PLANT BIOLOGY 2022; 22:580. [PMID: 36510137 PMCID: PMC9746204 DOI: 10.1186/s12870-022-03960-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 11/24/2022] [Indexed: 05/02/2023]
Abstract
BACKGROUND Characterization of the key factors determining gene expression level has been of significant interest. Previous studies on the relationship among evolutionary rates, codon usage bias, and expression level mostly focused on either nuclear genes or unicellular/multicellular organisms but few in chloroplast (cp) genes. Ophioglossum vulgatum is a unique fern and has important scientific and medicinal values. In this study, we sequenced its cp genome and transcriptome to estimate the evolutionary rates (dN and dS), selective pressure (dN/dS), gene expression level, codon usage bias, and their correlations. RESULTS The correlation coefficients between dN, dS, and dN/dS, and Transcripts Per Million (TPM) average values were -0.278 (P = 0.027 < 0.05), -0.331 (P = 0.008 < 0.05), and -0.311 (P = 0.013 < 0.05), respectively. The codon adaptation index (CAI) and tRNA adaptation index (tAI) were significantly positively correlated with TPM average values (P < 0.05). CONCLUSIONS Our results indicated that when the gene expression level was higher, the evolutionary rates and selective pressure were lower, but the codon usage bias was stronger. We provided evidence from cp gene data which supported the E-R (E stands for gene expression level and R stands for evolutionary rate) anti-correlation.
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Affiliation(s)
- Jing Hao
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yingyi Liang
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Jingyao Ping
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Jinye Li
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Wanxin Shi
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yingjuan Su
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
- Research Institute of Sun Yat-sen University in Shenzhen, Shenzhen, 518057, China.
| | - Ting Wang
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
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Li Y, Khandia R, Papadakis M, Alexiou A, Simonov AN, Khan AA. An investigation of codon usage pattern analysis in pancreatitis associated genes. BMC Genom Data 2022; 23:81. [PMID: 36434531 PMCID: PMC9700901 DOI: 10.1186/s12863-022-01089-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 10/10/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Pancreatitis is an inflammatory disorder resulting from the autoactivation of trypsinogen in the pancreas. The genetic basis of the disease is an old phenomenon, and evidence is accumulating for the involvement of synonymous/non-synonymous codon variants in disease initiation and progression. RESULTS The present study envisaged a panel of 26 genes involved in pancreatitis for their codon choices, compositional analysis, relative dinucleotide frequency, nucleotide disproportion, protein physical properties, gene expression, codon bias, and interrelated of all these factors. In this set of genes, gene length was positively correlated with nucleotide skews and codon usage bias. Codon usage of any gene is dependent upon its AT and GC component; however, AGG, CGT, and CGA encoding for Arg, TCG for Ser, GTC for Val, and CCA for Pro were independent of nucleotide compositions. In addition, Codon GTC showed a correlation with protein properties, isoelectric point, instability index, and frequency of basic amino acids. We also investigated the effect of various evolutionary forces in shaping the codon usage choices of genes. CONCLUSIONS This study will enable us to gain insight into the molecular signatures associated with the disease that might help identify more potential genes contributing to enhanced risk for pancreatitis. All the genes associated with pancreatitis are generally associated with physiological function, and mutations causing loss of function, over or under expression leads to an ailment. Therefore, the present study attempts to envisage the molecular signature in a group of genes that lead to pancreatitis in case of malfunction.
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Affiliation(s)
- Yuanyang Li
- Third-Grade Pharmacological Laboratory On Chinese Medicine Approved By State Administration of Traditional Chinese Medicine, Medical College of China Three Gorges, Yichang, China ,grid.254148.e0000 0001 0033 6389College of Medical Science, China Three Gorges University, Yichang, China
| | - Rekha Khandia
- grid.411530.20000 0001 0694 3745Department of Biochemistry and Genetics, Barkatullah University, Bhopal, MP 462026 India
| | - Marios Papadakis
- grid.412581.b0000 0000 9024 6397Department of Surgery II, University Hospital Witten-Herdecke, University of Witten-Herdecke, Heusnerstrasse 40, 42283 Wuppertal, Germany
| | - Athanasios Alexiou
- Department of Science and Engineering, Novel Global Community Educational Foundation, Hebersham, Australia ,AFNP Med Austria, Vienna, Austria
| | | | - Azmat Ali Khan
- grid.56302.320000 0004 1773 5396Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, 11451 Saudi Arabia
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Rossi R, Fang M, Zhu L, Jiang C, Yu C, Flesia C, Nie C, Li W, Ferlini A. Calculating and comparing codon usage values in rare disease genes highlights codon clustering with disease-and tissue- specific hierarchy. PLoS One 2022; 17:e0265469. [PMID: 35358230 PMCID: PMC8970475 DOI: 10.1371/journal.pone.0265469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 03/02/2022] [Indexed: 11/19/2022] Open
Abstract
We designed a novel strategy to define codon usage bias (CUB) in 6 specific small cohorts of human genes. We calculated codon usage (CU) values in 29 non-disease-causing (NDC) and 31 disease-causing (DC) human genes which are highly expressed in 3 distinct tissues, kidney, muscle, and skin. We applied our strategy to the same selected genes annotated in 15 mammalian species. We obtained CUB hierarchical clusters for each gene cohort which showed tissue-specific and disease-specific CUB fingerprints. We showed that DC genes (especially those expressed in muscle) display a low CUB, well recognizable in codon hierarchical clustering. We defined the extremely biased codons as "zero codons" and found that their number is significantly higher in all DC genes, all tissues, and that this trend is conserved across mammals. Based on this calculation in different gene cohorts, we identified 5 codons which are more differentially used across genes and mammals, underlining that some genes have favorite synonymous codons in use. Since of the muscle genes clear clusters, and, among these, dystrophin gene surprisingly does not show any "zero codon" we adopted a novel approach to study CUB, we called "mapping-on-codons". We positioned 2828 dystrophin missense and nonsense pathogenic variations on their respective codon, highlighting that its frequency and occurrence is not dependent on the CU values. We conclude our strategy consents to identify a hierarchical clustering of CU values in a gene cohort-specific fingerprints, with recognizable trend across mammals. In DC muscle genes also a disease-related fingerprint can be observed, allowing discrimination between DC and NDC genes. We propose that using our strategy which studies CU in specific gene cohorts, as rare disease genes, and tissue specific genes, may provide novel information about the CUB role in human and medical genetics, with implications on synonymous variations interpretation and codon optimization algorithms.
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Affiliation(s)
- Rachele Rossi
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
- Dubowitz Neuromuscular Unit, Institute of Child Health, University College London, London, United Kingdom
| | | | - Lin Zhu
- BGI-Shenzhen, Shenzhen, China
- BGI College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | | | - Cong Yu
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Cristina Flesia
- Department of Earth and Environment Science, University of Milano-Bicocca, Milano, Italy
| | | | | | - Alessandra Ferlini
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
- Dubowitz Neuromuscular Unit, Institute of Child Health, University College London, London, United Kingdom
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4
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Khandia R, Ali Khan A, Alexiou A, Povetkin SN, Nikolaevna VM. Codon Usage Analysis of Pro-Apoptotic Bim Gene Isoforms. J Alzheimers Dis 2022; 86:1711-1725. [DOI: 10.3233/jad-215691] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Background: Bim is a Bcl-2 homology 3 (BH3)-only proteins, a group of pro-apoptotic proteins involved in physiological and pathological conditions. Both the overexpression and under-expression of Bim protein are associated with the diseased condition, and various isoforms of Bim protein are present with differential apoptotic potential. Objective: The present study attempted to envisage the association of various molecular signatures with the codon choices of Bim isoforms. Methods: Molecular signatures like composition, codon usage, nucleotide skews, the free energy of mRNA transcript, physical properties of proteins, codon adaptation index, relative synonymous codon usage, and dinucleotide odds ratio were determined and analyzed for their associations with codon choices of Bim gene. Results: Skew analysis of the Bim gene indicated the preference of C nucleotide over G, A, and T and preference of G over T and A nucleotides was observed. An increase in C content at the first and third codon position increased gene expression while it decreased at the second codon position. Compositional constraints on nucleotide C at all three codon positions affected gene expression. The analysis revealed an exceptionally high usage of CpC dinucleotide in all the envisaged 31 isoforms of Bim. We correlated it with the requirement of rapid demethylation machinery to fine-tune the Bimgene expression. Also, mutational pressure played a dominant role in shaping codon usage bias in Bim isoforms. Conclusion: An exceptionally high usage of CpC dinucleotide in all the envisaged 31 isoforms of Bim indicates a high order selectional force to fine tune Bim gene expression.
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Affiliation(s)
- Rekha Khandia
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal, India
| | - Azmat Ali Khan
- Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Athanasios Alexiou
- Novel Global Community Educational Foundation, Australia & AFNP Med, Austria
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Zhao Z, Ma D. Genome-Wide Identification, Characterization and Function Analysis of Lineage-Specific Genes in the Tea Plant Camellia sinensis. Front Genet 2021; 12:770570. [PMID: 34858483 PMCID: PMC8631334 DOI: 10.3389/fgene.2021.770570] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 10/14/2021] [Indexed: 11/22/2022] Open
Abstract
Genes that have no homologous sequences with other species are called lineage-specific genes (LSGs), are common in living organisms, and have an important role in the generation of new functions, adaptive evolution and phenotypic alteration of species. Camellia sinensis var. sinensis (CSS) is one of the most widely distributed cultivars for quality green tea production. The rich catechins in tea have antioxidant, free radical elimination, fat loss and cancer prevention potential. To further understand the evolution and utilize the function of LSGs in tea, we performed a comparative genomics approach to identify Camellia-specific genes (CSGs). Our result reveals that 1701 CSGs were identified specific to CSS, accounting for 3.37% of all protein-coding genes. The majority of CSGs (57.08%) were generated by gene duplication, and the time of duplication occurrence coincide with the time of two genome-wide replication (WGD) events that happened in CSS genome. Gene structure analysis revealed that CSGs have shorter gene lengths, fewer exons, higher GC content and higher isoelectric point. Gene expression analysis showed that CSG had more tissue-specific expression compared to evolutionary conserved genes (ECs). Weighted gene co-expression network analysis (WGCNA) showed that 18 CSGs are mainly associated with catechin synthesis-related pathways, including phenylalanine biosynthesis, biosynthesis of amino acids, pentose phosphate pathway, photosynthesis and carbon metabolism. Besides, we found that the expression of three CSGs (CSS0030246, CSS0002298, and CSS0030939) was significantly down-regulated in response to both types of stresses (salt and drought). Our study first systematically identified LSGs in CSS, and comprehensively analyzed the features and potential functions of CSGs. We also identified key candidate genes, which will provide valuable assistance for further studies on catechin synthesis and provide a molecular basis for the excavation of excellent germplasm resources.
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Affiliation(s)
- Zhizhu Zhao
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Dongna Ma
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
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Srikulnath K, Ahmad SF, Singchat W, Panthum T. Why Do Some Vertebrates Have Microchromosomes? Cells 2021; 10:2182. [PMID: 34571831 PMCID: PMC8466491 DOI: 10.3390/cells10092182] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/17/2021] [Accepted: 08/17/2021] [Indexed: 12/27/2022] Open
Abstract
With more than 70,000 living species, vertebrates have a huge impact on the field of biology and research, including karyotype evolution. One prominent aspect of many vertebrate karyotypes is the enigmatic occurrence of tiny and often cytogenetically indistinguishable microchromosomes, which possess distinctive features compared to macrochromosomes. Why certain vertebrate species carry these microchromosomes in some lineages while others do not, and how they evolve remain open questions. New studies have shown that microchromosomes exhibit certain unique characteristics of genome structure and organization, such as high gene densities, low heterochromatin levels, and high rates of recombination. Our review focuses on recent concepts to expand current knowledge on the dynamic nature of karyotype evolution in vertebrates, raising important questions regarding the evolutionary origins and ramifications of microchromosomes. We introduce the basic karyotypic features to clarify the size, shape, and morphology of macro- and microchromosomes and report their distribution across different lineages. Finally, we characterize the mechanisms of different evolutionary forces underlying the origin and evolution of microchromosomes.
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Affiliation(s)
- Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (T.P.)
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- The International Undergraduate Program in Bioscience and Technology, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Amphibian Research Center, Hiroshima University, 1-3-1, Kagamiyama, Higashihiroshima 739-8526, Japan
| | - Syed Farhan Ahmad
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (T.P.)
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- The International Undergraduate Program in Bioscience and Technology, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Worapong Singchat
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (T.P.)
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Thitipong Panthum
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (T.P.)
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
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7
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Niczyporuk JS, Kozdrun W, Czekaj H, Stys-Fijol N. Fowl adenovirus strains 1/A and 11/D isolated from birds with reovirus infection. PLoS One 2021; 16:e0256137. [PMID: 34411166 PMCID: PMC8376056 DOI: 10.1371/journal.pone.0256137] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/29/2021] [Indexed: 11/18/2022] Open
Abstract
Inclusion body hepatitis (IBH) is, in some cases, a fatal disease affecting fowl by adenovirus strains which are subdivided into 5 species (A-E). In the current study, we investigated sequences from the Loop L1 region of the hexon gene of sequences of adenovirus field stains 1/A and 11/D isolated from a poultry flock co-infected with IBH and avian reoviruses ARVs. In early 2021, an epidemiologic survey highlighted the coinfection adenoviruses with other viruses (orthoreovirus infection) as being particularly deleterious within the poultry industry. Here, we investigated the Loop L1 HVR1-4 region of the hexon gene with relative synonymous codon usage (RSCU) designation and RSCU inclusive of all the mutations. These are the first results that have been presented on fowl adenovirus species A and D with simultaneous reovirus infection in 38-days old broiler chickens in Poland.
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Affiliation(s)
| | - Wojciech Kozdrun
- Department of Poultry Diseases, National Veterinary Research Institute, Pulawy, Poland
| | - Hanna Czekaj
- Department of Poultry Diseases, National Veterinary Research Institute, Pulawy, Poland
| | - Natalia Stys-Fijol
- Department of Poultry Diseases, National Veterinary Research Institute, Pulawy, Poland
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8
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Ma D, Ding Q, Guo Z, Zhao Z, Wei L, Li Y, Song S, Zheng HL. Identification, characterization and expression analysis of lineage-specific genes within mangrove species Aegiceras corniculatum. Mol Genet Genomics 2021; 296:1235-1247. [PMID: 34363105 DOI: 10.1007/s00438-021-01810-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 07/22/2021] [Indexed: 11/25/2022]
Abstract
Lineage-specific genes (LSGs) are the genes that have no recognizable homology to any sequences in other species, which are important drivers for the generation of new functions, phenotypic changes, and facilitating species adaptation to environment. Aegiceras corniculatum is one of major mangrove plant species adapted to waterlogging and saline conditions, and the exploration of aegiceras-specific genes (ASGs) is important to reveal its adaptation to the harsh environment. Here, we performed a systematic analysis on ASGs, focusing on their sequence characterization, origination and expression patterns. Our results reveal that there are 4823 ASGs in the genome, approximately 11.84% of all protein-coding genes. High proportion (45.78%) of ASGs originate from gene duplication, and the time of gene duplication of ASGs is consistent with the timing of two genome-wide replication (WGD) events that occurred in A. corniculatum, and also coincides with a short period of global warming during the Paleocene-Eocene Maximum (PETM, 55.5 million years ago). Gene structure analysis showed that ASGs have shorter protein lengths, fewer exons, and higher isoelectric point. Expression patterns analysis showed that ASGs had low levels of expression and more tissue-specific expression. Weighted gene co-expression network analysis (WGCNA) revealed that 86 ASGs co-expressed gene modules were primarily involved in pathways related to adversity stress, including plant hormone signal transduction, phenylpropanoid biosynthesis, photosynthesis, peroxisome and pentose phosphate pathway. This study provides a comprehensive analysis of the characteristics and potential functions of ASGs and identifies key candidate genes, which will contribute to the subsequent further investigation of the adaptation of A. corniculatum to intertidal coastal wetland habitats.
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Affiliation(s)
- Dongna Ma
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Qiansu Ding
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Zejun Guo
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Zhizhu Zhao
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Liufeng Wei
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Yiying Li
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shiwei Song
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Hai-Lei Zheng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China.
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Auboeuf D. The Physics-Biology continuum challenges darwinism: Evolution is directed by the homeostasis-dependent bidirectional relation between genome and phenotype. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 167:121-139. [PMID: 34097984 DOI: 10.1016/j.pbiomolbio.2021.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 05/19/2021] [Accepted: 05/31/2021] [Indexed: 10/21/2022]
Abstract
The physics-biology continuum relies on the fact that life emerged from prebiotic molecules. Here, I argue that life emerged from the coupling between nucleic acid and protein synthesis during which proteins (or proto-phenotypes) maintained the physicochemical parameter equilibria (or proto-homeostasis) in the proximity of their encoding nucleic acids (or proto-genomes). This protected the proto-genome physicochemical integrity (i.e., atomic composition) from environmental physicochemical constraints, and therefore increased the probability of reproducing the proto-genome without variation. From there, genomes evolved depending on the biological activities they generated in response to environmental fluctuations. Thus, a genome maintaining homeostasis (i.e., internal physicochemical parameter equilibria), despite and in response to environmental fluctuations, maintains its physicochemical integrity and has therefore a higher probability to be reproduced without variation. Consequently, descendants have a higher probability to share the same phenotype than their parents. Otherwise, the genome is modified during replication as a consequence of the imbalance of the internal physicochemical parameters it generates, until new mutation-deriving biological activities maintain homeostasis in offspring. In summary, evolution depends on feedforward and feedback loops between genome and phenotype, as the internal physicochemical conditions that a genome generates ─ through its derived phenotype in response to environmental fluctuations ─ in turn either guarantee its stability or direct its variation. Evolution may not be explained by the Darwinism-derived, unidirectional principle (random mutations-phenotypes-natural selection) but rather by the bidirectional relationship between genome and phenotype, in which the phenotype in interaction with the environment directs the evolution of the genome it derives from.
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Affiliation(s)
- Didier Auboeuf
- ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 Allée D'Italie, Site Jacques Monod, F-69007, Lyon, France.
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10
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Bayoumi A, Elsayed A, Han S, Petta S, Adams LA, Aller R, Khan A, García‐Monzón C, Arias‐Loste MT, Miele L, Latchoumanin O, Alenizi S, Gallego‐Durán R, Fischer J, Berg T, Craxì A, Metwally M, Qiao L, Liddle C, Yki‐Järvinen H, Bugianesi E, Romero‐Gomez M, George J, Eslam M. Mistranslation Drives Alterations in Protein Levels and the Effects of a Synonymous Variant at the Fibroblast Growth Factor 21 Locus. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2004168. [PMID: 34141520 PMCID: PMC8188187 DOI: 10.1002/advs.202004168] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 02/09/2021] [Indexed: 05/08/2023]
Abstract
Fibroblast growth factor 21 (FGF21) is a liver-derived hormone with pleiotropic beneficial effects on metabolism. Paradoxically, FGF21 levels are elevated in metabolic diseases. Interventions that restore metabolic homeostasis reduce FGF21. Whether abnormalities in FGF21 secretion or resistance in peripheral tissues is the initiating factor in altering FGF21 levels and function in humans is unknown. A genetic approach is used to help resolve this paradox. The authors demonstrate that the primary event in dysmetabolic phenotypes is the elevation of FGF21 secretion. The latter is regulated by translational reprogramming in a genotype- and context-dependent manner. To relate the findings to tissues outcomes, the minor (A) allele of rs838133 is shown to be associated with increased hepatic inflammation in patients with metabolic associated fatty liver disease. The results here highlight a dominant role for translation of the FGF21 protein to explain variations in blood levels that is at least partially inherited. These results provide a framework for translational reprogramming of FGF21 to treat metabolic diseases.
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Affiliation(s)
- Ali Bayoumi
- Storr Liver CentreWestmead Institute for Medical ResearchWestmead Hospital and University of SydneyWestmeadNSW2145Australia
| | - Asmaa Elsayed
- Storr Liver CentreWestmead Institute for Medical ResearchWestmead Hospital and University of SydneyWestmeadNSW2145Australia
| | - Shuanglin Han
- Storr Liver CentreWestmead Institute for Medical ResearchWestmead Hospital and University of SydneyWestmeadNSW2145Australia
| | - Salvatore Petta
- Section of Gastroenterology and HepatologyPROMISEUniversity of PalermoPalermo90133Italy
| | - Leon A. Adams
- Medical SchoolSir Charles Gairdner Hospital UnitUniversity of Western AustraliaNedlandsWA6009Australia
| | - Rocio Aller
- GastroenterologyHospital Clinico Universitario de ValladolidSchool of MedicineValladolid UniversityValladolid47002Spain
| | - Anis Khan
- Storr Liver CentreWestmead Institute for Medical ResearchWestmead Hospital and University of SydneyWestmeadNSW2145Australia
| | - Carmelo García‐Monzón
- Liver Research UnitInstituto de Investigacion Sanitaria PrincesaUniversity Hospital Santa CristinaCIBERehdMadrid28009Spain
| | - María Teresa Arias‐Loste
- Gastroenterology and Hepatology DepartmentMarqués de Valdecilla University HospitalSantander39008Spain
| | - Luca Miele
- Department of Internal MedicineCatholic University of the Sacred HeartRome20123Italy
| | - Olivier Latchoumanin
- Storr Liver CentreWestmead Institute for Medical ResearchWestmead Hospital and University of SydneyWestmeadNSW2145Australia
| | - Shafi Alenizi
- Storr Liver CentreWestmead Institute for Medical ResearchWestmead Hospital and University of SydneyWestmeadNSW2145Australia
| | - Rocio Gallego‐Durán
- Virgen del Rocío University HospitalInstitute of Biomedicine of SevilleSevilla41013Spain
| | - Janett Fischer
- Division of HepatologyDepartment of Medicine IILeipzig University Medical CenterLeipzig04103Germany
| | - Thomas Berg
- Division of HepatologyDepartment of Medicine IILeipzig University Medical CenterLeipzig04103Germany
| | - Antonio Craxì
- Section of Gastroenterology and HepatologyPROMISEUniversity of PalermoPalermo90133Italy
| | - Mayada Metwally
- Storr Liver CentreWestmead Institute for Medical ResearchWestmead Hospital and University of SydneyWestmeadNSW2145Australia
| | - Liang Qiao
- Storr Liver CentreWestmead Institute for Medical ResearchWestmead Hospital and University of SydneyWestmeadNSW2145Australia
| | - Christopher Liddle
- Storr Liver CentreWestmead Institute for Medical ResearchWestmead Hospital and University of SydneyWestmeadNSW2145Australia
| | - Hannele Yki‐Järvinen
- Department of MedicineUniversity of Helsinki and Helsinki University Hospital and Minerva Foundation Institute for Medical ResearchHelsinki00290Finland
| | - Elisabetta Bugianesi
- Division of GastroenterologyDepartment of Medical ScienceUniversity of TurinTurin10124Italy
| | - Manuel Romero‐Gomez
- Virgen del Rocío University HospitalInstitute of Biomedicine of SevilleSevilla41013Spain
| | - Jacob George
- Storr Liver CentreWestmead Institute for Medical ResearchWestmead Hospital and University of SydneyWestmeadNSW2145Australia
| | - Mohammed Eslam
- Storr Liver CentreWestmead Institute for Medical ResearchWestmead Hospital and University of SydneyWestmeadNSW2145Australia
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11
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Niczyporuk JS, Kozdrun W, Czekaj H, Piekarska K, Stys-Fijol N. Characterisation of adenovirus strains represented species B and E isolated from broiler chicken flocks in eastern Poland. Heliyon 2021; 7:e06225. [PMID: 33665417 PMCID: PMC7903317 DOI: 10.1016/j.heliyon.2021.e06225] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/11/2020] [Accepted: 02/03/2021] [Indexed: 11/19/2022] Open
Abstract
Fowl adenovirus strains were isolated from the internal organs of 3-wk-old broiler flocks exhibited clinical signs associated with inclusion body hepatitis (IBH). The isolated strains were molecularly characterised and sequencing revealed three distinct clusters. One cluster showed close proximity at the nucleotide level with adenovirus type/species - 6/E, 7/E, 8a/E, and 8b/E. The second cluster contained five reference sequences belonging to the species FAdV-D and E. A third cluster contained one field and four reference sequences belonging to the FAdV-5/B, FAdV-4/C, FAdV-2/D, and FAdV-1/A type/species respectively. The heterogenicity, Relative Synonymous Codon Usage (RSCU), codon composition, and nucleotide frequencies were examined. Statistical analyses, were carried out. The maximum likelihoods for the examined sequences were estimated. The data indicated that correlation between isolated of adenovirus type/species 5/B, and E in Poland have been presented. Indicated adenovirus types and their combinations with locally circulating FAdVs strains could have implications for current detection methods and pathogenicity on infected chickens.
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12
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McKinnon LM, Miller JB, Whiting MF, Kauwe JSK, Ridge PG. A comprehensive analysis of the phylogenetic signal in ramp sequences in 211 vertebrates. Sci Rep 2021; 11:622. [PMID: 33436653 PMCID: PMC7803996 DOI: 10.1038/s41598-020-78803-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 11/23/2020] [Indexed: 01/24/2023] Open
Abstract
Ramp sequences increase translational speed and accuracy when rare, slowly-translated codons are found at the beginnings of genes. Here, the results of the first analysis of ramp sequences in a phylogenetic construct are presented. Ramp sequences were compared from 247 vertebrates (114 Mammalian and 133 non-mammalian), where the presence and absence of ramp sequences was analyzed as a binary character in a parsimony and maximum likelihood framework. Additionally, ramp sequences were mapped to the Open Tree of Life synthetic tree to determine the number of parallelisms and reversals that occurred, and those results were compared to random permutations. Parsimony and maximum likelihood analyses of the presence and absence of ramp sequences recovered phylogenies that are highly congruent with established phylogenies. Additionally, 81% of vertebrate mammalian ramps and 81.2% of other vertebrate ramps had less parallelisms and reversals than the mean from 1000 randomly permuted trees. A chi-square analysis of completely orthologous ramp sequences resulted in a p-value < 0.001 as compared to random chance. Ramp sequences recover comparable phylogenies as other phylogenomic methods. Although not all ramp sequences appear to have a phylogenetic signal, more ramp sequences track speciation than expected by random chance. Therefore, ramp sequences may be used in conjunction with other phylogenomic approaches if many orthologs are taken into account. However, phylogenomic methods utilizing few orthologs should be cautious in incorporating ramp sequences because individual ramp sequences may provide conflicting signals.
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Affiliation(s)
- Lauren M McKinnon
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA
| | - Justin B Miller
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA
| | - Michael F Whiting
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA
- Monte L. Bean Museum, Brigham Young University, Provo, UT, 84602, USA
| | - John S K Kauwe
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA
| | - Perry G Ridge
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA.
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Lee J, Hong SE. Functional annotation of de novo variants from healthy individuals. Genomics Inform 2019; 17:e46. [PMID: 31896246 PMCID: PMC6944041 DOI: 10.5808/gi.2019.17.4.e46] [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: 11/19/2019] [Accepted: 12/05/2019] [Indexed: 11/27/2022] Open
Abstract
The implications of germline de novo variants (DNVs) in diseases are well documented. Despite extensive research, inconsistencies between studies remain a challenge, and the distribution and genetic characteristics of DNVs need to be precisely evaluated. To address this issue at the whole-genome scale, a large number of DNVs identified from the whole-genome sequencing of 1,902 healthy trios (i.e., parents and progeny) from the Simons Foundation for Autism Research Initiative study and 20 healthy Korean trios were analyzed. These apparently nonpathogenic DNVs were enriched in functional elements of the genome but relatively depleted in regions of common copy number variants, implying their potential function as triggers of evolution even in healthy groups. No strong mutational hotspots were identified. The pathogenicity of the DNVs was not strongly elevated, reflecting the health status of the cohort. The mutational signatures were consistent with previous studies. This study will serve as a reference for future DNV studies.
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Affiliation(s)
- Jean Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Sung Eun Hong
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea
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14
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Pathogenic potential of non-typhoidal Salmonella serovars isolated from aquatic environments in Mexico. Genes Genomics 2019; 41:767-779. [DOI: 10.1007/s13258-019-00798-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 02/19/2019] [Indexed: 12/20/2022]
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