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Hurali DT, Banerjee M, Ballal A. Unravelling the involvement of protein disorder in cyanobacterial stress responses. Int J Biol Macromol 2024; 277:133934. [PMID: 39025183 DOI: 10.1016/j.ijbiomac.2024.133934] [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: 05/10/2024] [Revised: 07/09/2024] [Accepted: 07/15/2024] [Indexed: 07/20/2024]
Abstract
This study has explored the involvement of Intrinsically Disordered Proteins (IDPs) in cyanobacterial stress response. IDPs possess distinct physicochemical properties, which allow them to execute diverse functions. Anabaena PCC 7120, the model photosynthetic, nitrogen-fixing cyanobacterium encodes 688 proteins (11 % of the total proteome) with at least one intrinsically disordered region (IDR). Of these, 130 proteins that showed >30 % overall disorder were designated as IDPs. Physico-chemical analysis, showed these IDPs to adopt shapes ranging from 'globular' to 'tadpole-like'. Upon exposure to NaCl, 41 IDP-encoding genes were found to be differentially expressed. Surprisingly, most of these were induced, indicating the importance of IDP-accumulation in overcoming salt stress. Subsequently, six IDPs were identified to be induced by multiple stresses (salt, ammonium and selenite). Interestingly, the presence of these 6-multiple stress-induced IDPs was conserved in filamentous cyanobacteria. Utilizing the experimental proteomic data of Anabaena, these 6 IDPs were found to interact with many proteins involved in diverse pathways, underscoring their physiological importance as protein hubs. This study lays the framework for IDP-related research in Anabaena by (a) identifying, as well as physiochemically characterizing, all the disordered proteins and (b) uncovering a subset of IDPs that are likely to be critical in adaptation to environmental stresses.
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Affiliation(s)
- Deepak T Hurali
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai 400094, India
| | - Manisha Banerjee
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai 400094, India.
| | - Anand Ballal
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai 400094, India.
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Kang T, Choi YJ, Kim J, Park HJ, Jang WJ. Whole genome sequence and comparative genomic analysis of novel Rickettsia koreansis strain CNH17-7 isolated from human. Eur J Clin Microbiol Infect Dis 2024:10.1007/s10096-024-04876-x. [PMID: 39031268 DOI: 10.1007/s10096-024-04876-x] [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: 04/19/2024] [Accepted: 06/15/2024] [Indexed: 07/22/2024]
Abstract
PURPOSE To determine the genomic feature of novel spotted fever-causing Rickettsia koreansis strain CNH17-7, which is different from R. japonica that is a causative agent for Japanese spotted fever (JSF), and to perform its comparative genomic analysis. METHODS Whole genome sequencing (WGS) was performed on R. koreansis strain CNH17-7 by using the Illumina Miseq system. After WGS, assembly and annotation were done by SPAdes. Then, its genomic features were compared with 19 different Rickettsia species. Based on the average nucleotide identity (ANI) value, an unweighted pair group method with an arithmetic mean (UPGMA) dendrogram was generated. Following the dendrogram analysis, pan-and core-genome analysis was performed. Then additional comparative analyses with two genetically closest Rickettsia species were conducted based on gene repertoire. RESULTS R. koreansis strain CNH17-7 has a chromosome consisting of 1,392,633 bp with GC content of 32.4%. The ANI-derived UPGMA showed that R. koreansis strain CNH17-7 is genetically close to R. japonica YH and R. heilongjiangensis 054 but is distinctively differentiated. The ANI value of R. koreansis strain CNH17-7 to R. japonica YH and R. heilongjiangensis 054 are 98.14% and 98.04% respectively, indicating R. koreansis strain CNH17-7 is sufficient to be classified as a new species. Other than ANI, R. koreansis strain CNH17-7 also contains novel CDS and its COG functional category proportion which is distinct compared to R. japonica YH and R. heilongjiangensis 054. CONCLUSION We have revealed genomic features of the novel R. koreansis strain CNH17-7. Hence, we propose R. koreansis strain CNH17-7 as new Rickettsia species.
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Affiliation(s)
- Taeuk Kang
- Department of Microbiology, Konkuk University School of Medicine, College of Medicine, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
- Research Institute of Medical Science, Konkuk University School of Medicine, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
| | - Yeon-Joo Choi
- Department of Microbiology, Konkuk University School of Medicine, College of Medicine, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
- Research Institute of Medical Science, Konkuk University School of Medicine, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
| | - Jeoungyeon Kim
- Department of Microbiology, Konkuk University School of Medicine, College of Medicine, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
- Research Institute of Medical Science, Konkuk University School of Medicine, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
| | - Hye-Jin Park
- Department of Microbiology, Konkuk University School of Medicine, College of Medicine, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
- Research Institute of Medical Science, Konkuk University School of Medicine, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
| | - Won-Jong Jang
- Department of Microbiology, Konkuk University School of Medicine, College of Medicine, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea.
- Research Institute of Medical Science, Konkuk University School of Medicine, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea.
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Krappinger JC, Aguilar Gomez CM, Hoenikl A, Schusterbauer V, Hatzl AM, Feichtinger J, Glieder A. dMAD7 is a promising tool for targeted gene regulation in the methylotrophic yeast Komagataella phaffii. N Biotechnol 2024; 83:110-120. [PMID: 38960022 DOI: 10.1016/j.nbt.2024.06.008] [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: 03/27/2024] [Revised: 06/07/2024] [Accepted: 06/30/2024] [Indexed: 07/05/2024]
Abstract
The methylotrophic yeast Komagataella phaffii is a popular host system for the pharmaceutical and biotechnological production of recombinant proteins. CRISPR-Cas9 and its derivative CRISPR interference (CRISPRi) offer a promising avenue to further enhance and exploit the full capabilities of this host. MAD7 and its catalytically inactive variant "dead" MAD7 (dMAD7) represent an interesting alternative to established CRISPR-Cas9 systems and are free to use for industrial and academic research. CRISPRi utilizing dMAD7 does not introduce double-strand breaks but only binds to the DNA to regulate gene expression. Here, we report the first use of dMAD7 in K. phaffii to regulate the expression of the enhanced green fluorescent protein (eGFP). A reduction of eGFP fluorescence level (up to 88 %) was achieved in random integration experiments using dMAD7 plasmids. Integration loci/events of investigated strains were assessed through whole genome sequencing. Additionally, RNA-sequencing experiments corroborated the whole genome sequencing results and showed a significantly reduced expression of eGFP in strains containing a dMAD7 plasmid, among others. Our findings conclusively demonstrate the utility of dMAD7 in K. phaffii through successfully regulating eGFP expression.
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Affiliation(s)
- Julian C Krappinger
- Christian Doppler Laboratory for Innovative Pichia pastoris Host and Vector Systems, Graz, Austria; Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria
| | - Carla M Aguilar Gomez
- Christian Doppler Laboratory for Innovative Pichia pastoris Host and Vector Systems, Graz, Austria; Institute of Molecular Biotechnology, Graz University of Technology, Graz, Austria
| | - Andrea Hoenikl
- Institute of Molecular Biotechnology, Graz University of Technology, Graz, Austria
| | | | - Anna-Maria Hatzl
- Christian Doppler Laboratory for Innovative Pichia pastoris Host and Vector Systems, Graz, Austria; Institute of Molecular Biotechnology, Graz University of Technology, Graz, Austria
| | - Julia Feichtinger
- Christian Doppler Laboratory for Innovative Pichia pastoris Host and Vector Systems, Graz, Austria; Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria.
| | - Anton Glieder
- Christian Doppler Laboratory for Innovative Pichia pastoris Host and Vector Systems, Graz, Austria; Institute of Molecular Biotechnology, Graz University of Technology, Graz, Austria
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Chandel N, Somvanshi PR, Thakur V. Characterisation of Indian gut microbiome for B-vitamin production and its comparison with Chinese cohort. Br J Nutr 2024; 131:686-697. [PMID: 37781761 PMCID: PMC10803823 DOI: 10.1017/s0007114523002179] [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: 05/04/2023] [Revised: 09/21/2023] [Accepted: 09/27/2023] [Indexed: 10/03/2023]
Abstract
The human gut microbiota can biosynthesize essential micronutrients such as B-vitamins and is also known for its metabolic cooperative behaviour. The present study characterises such B-vitamin biosynthesizers, their biosynthetic pathways, explores their prevalence and abundance, examines how lifestyle or diet affects them in multiple Indian cohorts and compares it with the Chinese cohort. To achieve this, publicly available faecal metagenome data of healthy individuals from multiple Indian (two urban and three tribal populations) and a Chinese cohort were analysed. The distribution of prevalence and abundance of B-vitamin biosynthesizers showed similar profiles to that of the entire gut community of the Indian cohort, and there were 28 B-vitamin biosynthesizers that had modest or higher prevalence and abundance. The omnivorous diet affected only the prevalence of a few B-vitamin biosynthesizers; however, lifestyle and/or location affected both prevalence and abundance. A comparison with the Chinese cohort showed that fourteen B-vitamin biosynthesizers were significantly more prevalent and abundant in Chinese as compared with Indian samples (False Discovery Rate (FDR) <= 0·05). The metabolic potential of the entire gut community for B-vitamin production showed that within India, the tribal cohort has a higher abundance of B-vitamin biosynthesis pathways as compared with two urban cohorts namely, Bhopal and Kasargod, and comparison with the Chinese cohort revealed a higher abundance in the latter group. Potential metabolic cooperative behaviour of the Indian gut microbiome for biosynthesis of the B-vitamins showed multiple pairs of species showed theoretical complementarity for complete biosynthetic pathways genes of thiamine, riboflavin, niacin and pantothenate.
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Affiliation(s)
- Nisha Chandel
- Department of Systems and Computational Biology, University of Hyderabad, Gachibowli, Hyderabad, 500046, India
| | - Pramod R. Somvanshi
- Department of Systems and Computational Biology, University of Hyderabad, Gachibowli, Hyderabad, 500046, India
| | - Vivek Thakur
- Department of Systems and Computational Biology, University of Hyderabad, Gachibowli, Hyderabad, 500046, India
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Graf J, Schöpperle M, Pernil R, Schleiff E. Two TonB-dependent outer membrane transporters involved in heme uptake in Anabaena sp. PCC 7120. MICROBIAL CELL (GRAZ, AUSTRIA) 2024; 11:16-28. [PMID: 38234586 PMCID: PMC10792254 DOI: 10.15698/mic2024.01.812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 11/03/2023] [Accepted: 11/13/2023] [Indexed: 01/19/2024]
Abstract
Low availability of micronutrients such as iron has enforced the evolution of uptake systems in all kingdoms of life. In Gram-negative bacteria, outer membrane, periplasmatic and plasma membrane localized proteins facilitate the uptake of iron-loaded chelators, which are energized by TonB proteins. The specificity of different uptake systems likely depends either on the endogenously produced siderophore or on the bioavailability of iron-chelator complexes in the environment. Hence, an uptake system for schizokinen produced by the model cyanobacterium Anabaena sp. PCC 7120 exists, while bioinformatics analysis suggests the existence of additional systems, likely for uptake of xenosiderophores. Consistently, proteins encoded by alr2153 (hutA1) and alr3242 (hutA2) are assigned as outer membrane heme transporters. Indeed, Anabaena sp. PCC 7120 can utilize external heme as an iron source. The addition of heme resulted in an induction of genes involved in heme degradation and chlorophyll a synthesis and in an increase of the chlorophyll a content. Moreover, iron starvation induced the expression of hutA1, while the addition of heme led to its repression. Remarkably, the addition of a high concentration of heme but not iron starvation resulted in hutA2 induction. Plasmid insertion mutants of both genes exhibited a reduced capacity to recover from iron starvation by heme addition, which indicates a dependence of heme uptake on functional HutA1 and HutA2 proteins. The structural model generated by bioinformatics methods is further in agreement with a role in heme uptake. Thus, we provide evidence that Anabaena sp. PCC 7120 uses a heme uptake system in parallel to other iron acquisition systems.
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Affiliation(s)
- Julia Graf
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max von Laue Str. 9, 60438 Frankfurt, Germany
| | - Martin Schöpperle
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max von Laue Str. 9, 60438 Frankfurt, Germany
- Current address: Lonza Cologne GmbH, Köln, Germany:
| | - Rafael Pernil
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max von Laue Str. 9, 60438 Frankfurt, Germany
| | - Enrico Schleiff
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max von Laue Str. 9, 60438 Frankfurt, Germany
- Frankfurt Institute for Advanced Studies, Ruth-Moufang-Straße 1, 60438 Frankfurt, Germany
- Buchmann Institute for Molecular Life Sciences, Max von Laue Str. 11, 60438 Frankfurt, Germany
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6
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Kim YH, Park J, Chung HS. Genetic characterization of tetracycline-resistant Staphylococcus aureus with reduced vancomycin susceptibility using whole-genome sequencing. Arch Microbiol 2023; 206:24. [PMID: 38103051 DOI: 10.1007/s00203-023-03760-0] [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: 07/21/2023] [Revised: 11/09/2023] [Accepted: 11/19/2023] [Indexed: 12/17/2023]
Abstract
This study aimed to analyze the genetic characteristics of Staphylococcus aureus with reduced vancomycin susceptibility (RVS-SA). Whole-genome sequencing was performed on 27 RVS-SA clinical isolates, and comparative genomic analysis was performed using S. aureus reference strains. Pan-genome orthologous groups (POGs) were identified that were present in RVS-SA but absent in the reference strains, but further analysis showed that the presence of these POGs was influenced by tetracycline resistance rather than vancomycin resistance. Therefore, we restricted our analysis to tetracycline-resistant (tetR) RVS-SA and tetR vancomycin-susceptible S. aureus (VSSA). Phylogenomic analysis showed them to be closely related, and further analysis revealed the presence of an uncharacterized protein SAB0394 and the absence of lytA in tetR RVS-SA, which are involved in cell wall thickening. In summary, using whole-genome sequencing we identified gain or loss of genes in tetR RVS-SA strains. These findings provide insights into the investigation of mechanisms associated with reduced vancomycin susceptibility and have the potential to contribute to the development of molecular biomarkers for the rapid and efficient detection of RVS-SA.
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Affiliation(s)
- Yu-Hee Kim
- Advanced Biomedical Research Institute, Ewha Womans University Seoul Hospital, Seoul, Korea
- Ewha Education and Research Center for Infection, Ewha Womans University Medical Center, Seoul, Korea
| | - Junghun Park
- Ewha Education and Research Center for Infection, Ewha Womans University Medical Center, Seoul, Korea
| | - Hae-Sun Chung
- Ewha Education and Research Center for Infection, Ewha Womans University Medical Center, Seoul, Korea.
- Department of Laboratory Medicine, Ewha Womans University College of Medicine, 25 Magokdong-ro 2-gil, Gangseo-gu, Seoul, 07804, Republic of Korea.
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7
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Klemm P, Stadler PF, Lechner M. Proteinortho6: pseudo-reciprocal best alignment heuristic for graph-based detection of (co-)orthologs. FRONTIERS IN BIOINFORMATICS 2023; 3:1322477. [PMID: 38152702 PMCID: PMC10751348 DOI: 10.3389/fbinf.2023.1322477] [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: 10/16/2023] [Accepted: 11/06/2023] [Indexed: 12/29/2023] Open
Abstract
Proteinortho is a widely used tool to predict (co)-orthologous groups of genes for any set of species. It finds application in comparative and functional genomics, phylogenomics, and evolutionary reconstructions. With a rapidly increasing number of available genomes, the demand for large-scale predictions is also growing. In this contribution, we evaluate and implement major algorithmic improvements that significantly enhance the speed of the analysis without reducing precision. Graph-based detection of (co-)orthologs is typically based on a reciprocal best alignment heuristic that requires an all vs. all comparison of proteins from all species under study. The initial identification of similar proteins is accelerated by introducing an alternative search tool along with a revised search strategy-the pseudo-reciprocal best alignment heuristic-that reduces the number of required sequence comparisons by one-half. The clustering algorithm was reworked to efficiently decompose very large clusters and accelerate processing. Proteinortho6 reduces the overall processing time by an order of magnitude compared to its predecessor while maintaining its small memory footprint and good predictive quality.
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Affiliation(s)
- Paul Klemm
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany
| | - Peter F. Stadler
- Bioinformatics Group, Institute of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany
- Max-Planck-Institute for Mathematics in the Sciences, Leipzig, Germany
- Institute for Theoretical Chemistry, University of Vienna, Wien, Austria
- Facultad de Ciencias, Universidad National de Colombia, Bogotá, Colombia
- Santa Fe Institute, Santa Fe, NM, United States
| | - Marcus Lechner
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany
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8
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Nestor BJ, Bayer PE, Fernandez CGT, Edwards D, Finnegan PM. Approaches to increase the validity of gene family identification using manual homology search tools. Genetica 2023; 151:325-338. [PMID: 37817002 PMCID: PMC10692271 DOI: 10.1007/s10709-023-00196-8] [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: 06/07/2023] [Accepted: 10/01/2023] [Indexed: 10/12/2023]
Abstract
Identifying homologs is an important process in the analysis of genetic patterns underlying traits and evolutionary relationships among species. Analysis of gene families is often used to form and support hypotheses on genetic patterns such as gene presence, absence, or functional divergence which underlie traits examined in functional studies. These analyses often require precise identification of all members in a targeted gene family. Manual pipelines where homology search and orthology assignment tools are used separately are the most common approach for identifying small gene families where accurate identification of all members is important. The ability to curate sequences between steps in manual pipelines allows for simple and precise identification of all possible gene family members. However, the validity of such manual pipeline analyses is often decreased by inappropriate approaches to homology searches including too relaxed or stringent statistical thresholds, inappropriate query sequences, homology classification based on sequence similarity alone, and low-quality proteome or genome sequences. In this article, we propose several approaches to mitigate these issues and allow for precise identification of gene family members and support for hypotheses linking genetic patterns to functional traits.
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Affiliation(s)
- Benjamin J Nestor
- School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia.
- Centre for Applied Bioinformatics, University of Western Australia, Perth, WA, 6009, Australia.
| | - Philipp E Bayer
- School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia
- Centre for Applied Bioinformatics, University of Western Australia, Perth, WA, 6009, Australia
| | - Cassandria G Tay Fernandez
- School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia
- Centre for Applied Bioinformatics, University of Western Australia, Perth, WA, 6009, Australia
| | - David Edwards
- School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia
- Centre for Applied Bioinformatics, University of Western Australia, Perth, WA, 6009, Australia
| | - Patrick M Finnegan
- School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia
- Centre for Applied Bioinformatics, University of Western Australia, Perth, WA, 6009, Australia
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9
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Mamun MAA, Maruyama JI. Fungal transglutaminase domain-containing proteins are involved in hyphal protection at the septal pore against wounding. Mol Biol Cell 2023; 34:ar127. [PMID: 37756125 PMCID: PMC10848947 DOI: 10.1091/mbc.e23-01-0021] [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: 01/25/2023] [Revised: 09/12/2023] [Accepted: 09/22/2023] [Indexed: 09/29/2023] Open
Abstract
Transglutaminase (TG) is a ubiquitous enzyme that crosslinks substrates. In humans, TG participates in blood clotting and wound healing. However, the functions related to the cellular protection of microbial TG are unknown. In filamentous fungi, we previously identified SppB, which contains the transglutaminase core (TGc) domain and functions in hyphal protection at the septal pore upon wounding. Here, we further analyzed the cytokinesis-related protein Cyk3 and peptide N-glycanase Png1, as both contain the TGc domain. All three proteins exhibited functional importance in wound-related hyphal protection at the septal pore. Upon wounding, SppB and AoPng1 accumulated at the septal pore, whereas AoCyk3 and AoPng1 normally localized around the septal pore. The putative Cys-His-Asp catalytic triad of SppB is conserved with the human TGc domain-containing kyphoscoliosis peptidase. Catalytic triad disruptive mutants of SppB and AoCyk3 exhibited septal pore plugging defects. Similar to other TGs, SppB underwent wound-induced truncation of the N-terminal region. Notably, TG activity was detected in vivo at the septal pore of wounded hyphae using a fluorescent-labeled substrate; however, the activity was inhibited by the TG inhibitor cystamine. Our study suggests a conserved role for TGc domain-containing proteins in wound-related protection in fungi, similar to that in humans.
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Affiliation(s)
- Md. Abdulla Al Mamun
- Department of Biotechnology, The University of Tokyo, Tokyo 113-8657, Japan
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115
| | - Jun-ichi Maruyama
- Department of Biotechnology, The University of Tokyo, Tokyo 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113-8657, Japan
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10
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Al Mamun MA, Reza MA, Islam MS. Identification of novel proteins regulating lipid droplet biogenesis in filamentous fungi. Mol Microbiol 2023; 120:702-722. [PMID: 37748926 DOI: 10.1111/mmi.15170] [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: 03/02/2023] [Revised: 09/06/2023] [Accepted: 09/11/2023] [Indexed: 09/27/2023]
Abstract
Lipid droplets (LDs) are storage organelles for neutral lipids which are critical for lipid homeostasis. Current knowledge of fungal LD biogenesis is largely limited to budding yeast, while LD regulation in multinucleated filamentous fungi which exhibit considerable metabolic activity remains unexplored. In this study, 19 LD-associated proteins were identified in the multinucleated species Aspergillus oryzae using a colocalization screening of a previously established enhanced green fluorescent protein (EGFP) fusion library. Functional screening identified 12 lipid droplet-regulating (LDR) proteins whose loss of function resulted in irregular LD biogenesis, particularly in terms of LD number and size. Bioinformatics analysis, targeted mutagenesis, and microscopy revealed four LDR proteins that localize to LD via the putative amphipathic helices (AHs). Further analysis revealed that LdrA with an Opi1 domain is essential for cytoplasmic and nuclear LD biogenesis involving a novel AH. Phylogenetic analysis demonstrated that the patterns of gene evolution were predominantly based on gene duplication. Our study identified a set of novel proteins involved in the regulation of LD biogenesis, providing unique molecular and evolutionary insights into fungal lipid storage.
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Affiliation(s)
- Md Abdulla Al Mamun
- Department of Biotechnology, The University of Tokyo, Tokyo, Japan
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
| | - M Abu Reza
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
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11
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Persson Waller K, Myrenås M, Börjesson S, Kim H, Widerström M, Monsen T, Sigurðarson Sandholt AK, Östlund E, Cha W. Genotypic characterization of Staphylococcus chromogenes and Staphylococcus simulans from Swedish cases of bovine subclinical mastitis. J Dairy Sci 2023; 106:7991-8004. [PMID: 37641317 DOI: 10.3168/jds.2023-23523] [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: 03/22/2023] [Accepted: 05/23/2023] [Indexed: 08/31/2023]
Abstract
Staphylococcus chromogenes and Staphylococcus simulans are commonly found in intramammary infections (IMI) associated with bovine subclinical mastitis, but little is known about genotypic variation and relatedness within species. This includes knowledge about genes encoding antimicrobial resistance (AMR) and potential virulence factors (pVF). The aim of this study was therefore to investigate these aspects by whole-genome sequencing of milk isolates from Swedish dairy cows with subclinical mastitis in an observational study. We also wanted to study if specific genotypes were associated with persistent IMI and the inflammatory response at udder quarter level. In total, 105 and 118 isolates of S. chromogenes and S. simulans, respectively, were included. Isolates were characterized using a 7-locus multilocus sequence typing (7-MLST), core genome analysis and in-silico analysis of AMR and pVF genes. Forty-seven sequence types (ST) and 7 core genome clusters of S. chromogenes were identified, and the most common ST were ST-6 and ST-109, both belonging to cluster VII. A 7-locus MLST scheme for S. simulans was not available, but 3 core genome clusters and 5 subclusters were described. Overall, substantial variation in ST and clusters among cows and herds were found in both species. Some ST of S. chromogenes were found in several herds, indicating spread between herds. Moreover, within-herd spread of the same genotype was observed for both species. Only a few AMR genes [blaZ, strpS194, vga(A)] were detected in a limited number of isolates, with the exception of blaZ coding for β-lactamase, which was identified in 22% of the isolates of S. chromogenes with ST-19, ST-102, and ST-103 more commonly carrying this gene compared with other ST. However, the blaZ gene was not identified in S. simulans. The average total number of pVF detected per isolate was similar in S. chromogenes (n = 30) and S. simulans (n = 33), but some variation in total numbers and presence of specific pVF or functional groups of pVF, was shown between ST/clusters within species. Differences in inflammatory response and potentially in persistent IMI at udder quarter level were found between S. chromogenes subtypes but not between S. simulans subtypes. In conclusion, the results from the present study generates new insight into the epidemiology of bovine S. chromogenes and S. simulans IMI, which can have implications for future prevention and antimicrobial treatment of infections related to these species.
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Affiliation(s)
- K Persson Waller
- Department of Animal Health and Antimicrobial Strategies, National Veterinary Institute (SVA), SE-751 89 Uppsala, Sweden.
| | - M Myrenås
- Department of Animal Health and Antimicrobial Strategies, National Veterinary Institute (SVA), SE-751 89 Uppsala, Sweden
| | - S Börjesson
- School of Health Science, Örebro University, Örebro, SE-701 82, Sweden
| | - H Kim
- Department of Disease Control and Epidemiology, National Veterinary Institute (SVA), SE-751 89 Uppsala, Sweden
| | - M Widerström
- Department of Clinical Microbiology, Umeå University, Umeå SE-90185, Sweden
| | - T Monsen
- Department of Clinical Microbiology, Umeå University, Umeå SE-90185, Sweden
| | | | - E Östlund
- Department of Microbiology, National Veterinary Institute (SVA), SE-75189 Uppsala, Sweden
| | - W Cha
- Department of Disease Control and Epidemiology, National Veterinary Institute (SVA), SE-751 89 Uppsala, Sweden
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12
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Funabiki H, Wassing IE, Jia Q, Luo JD, Carroll T. Coevolution of the CDCA7-HELLS ICF-related nucleosome remodeling complex and DNA methyltransferases. eLife 2023; 12:RP86721. [PMID: 37769127 PMCID: PMC10538959 DOI: 10.7554/elife.86721] [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] [Indexed: 09/30/2023] Open
Abstract
5-Methylcytosine (5mC) and DNA methyltransferases (DNMTs) are broadly conserved in eukaryotes but are also frequently lost during evolution. The mammalian SNF2 family ATPase HELLS and its plant ortholog DDM1 are critical for maintaining 5mC. Mutations in HELLS, its activator CDCA7, and the de novo DNA methyltransferase DNMT3B, cause immunodeficiency-centromeric instability-facial anomalies (ICF) syndrome, a genetic disorder associated with the loss of DNA methylation. We here examine the coevolution of CDCA7, HELLS and DNMTs. While DNMT3, the maintenance DNA methyltransferase DNMT1, HELLS, and CDCA7 are all highly conserved in vertebrates and green plants, they are frequently co-lost in other evolutionary clades. The presence-absence patterns of these genes are not random; almost all CDCA7 harboring eukaryote species also have HELLS and DNMT1 (or another maintenance methyltransferase, DNMT5). Coevolution of presence-absence patterns (CoPAP) analysis in Ecdysozoa further indicates coevolutionary linkages among CDCA7, HELLS, DNMT1 and its activator UHRF1. We hypothesize that CDCA7 becomes dispensable in species that lost HELLS or DNA methylation, and/or the loss of CDCA7 triggers the replacement of DNA methylation by other chromatin regulation mechanisms. Our study suggests that a unique specialized role of CDCA7 in HELLS-dependent DNA methylation maintenance is broadly inherited from the last eukaryotic common ancestor.
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Affiliation(s)
- Hironori Funabiki
- Laboratory of Chromosome and Cell Biology, The Rockefeller UniversityNew YorkUnited States
| | - Isabel E Wassing
- Laboratory of Chromosome and Cell Biology, The Rockefeller UniversityNew YorkUnited States
| | - Qingyuan Jia
- Laboratory of Chromosome and Cell Biology, The Rockefeller UniversityNew YorkUnited States
| | - Ji-Dung Luo
- Bioinformatics Resource Center, The Rockefeller UniversityNew YorkUnited States
| | - Thomas Carroll
- Bioinformatics Resource Center, The Rockefeller UniversityNew YorkUnited States
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13
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Funabiki H, Wassing IE, Jia Q, Luo JD, Carroll T. Coevolution of the CDCA7-HELLS ICF-related nucleosome remodeling complex and DNA methyltransferases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.30.526367. [PMID: 36778482 PMCID: PMC9915587 DOI: 10.1101/2023.01.30.526367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
5-Methylcytosine (5mC) and DNA methyltransferases (DNMTs) are broadly conserved in eukaryotes but are also frequently lost during evolution. The mammalian SNF2 family ATPase HELLS and its plant ortholog DDM1 are critical for maintaining 5mC. Mutations in HELLS, its activator CDCA7, and the de novo DNA methyltransferase DNMT3B, cause immunodeficiency-centromeric instability-facial anomalies (ICF) syndrome, a genetic disorder associated with the loss of DNA methylation. We here examine the coevolution of CDCA7, HELLS and DNMTs. While DNMT3, the maintenance DNA methyltransferase DNMT1, HELLS, and CDCA7 are all highly conserved in vertebrates and green plants, they are frequently co-lost in other evolutionary clades. The presence-absence patterns of these genes are not random; almost all CDCA7 harboring eukaryote species also have HELLS and DNMT1 (or another maintenance methyltransferase, DNMT5). Coevolution of presence-absence patterns (CoPAP) analysis in Ecdysozoa further indicates coevolutionary linkages among CDCA7, HELLS, DNMT1 and its activator UHRF1. We hypothesize that CDCA7 becomes dispensable in species that lost HELLS or DNA methylation, and/or the loss of CDCA7 triggers the replacement of DNA methylation by other chromatin regulation mechanisms. Our study suggests that a unique specialized role of CDCA7 in HELLS-dependent DNA methylation maintenance is broadly inherited from the last eukaryotic common ancestor.
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Affiliation(s)
- Hironori Funabiki
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY 10065
| | - Isabel E. Wassing
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY 10065
| | - Qingyuan Jia
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY 10065
| | - Ji-Dung Luo
- Bioinformatics Resource Center, The Rockefeller University, New York, NY 10065
| | - Thomas Carroll
- Bioinformatics Resource Center, The Rockefeller University, New York, NY 10065
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14
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Robainas-Del-Pino Y, Viader-Salvadó JM, Herrera-Estala AL, Guerrero-Olazarán M. Functional characterization of the Komagataella phaffii 1033 gene promoter and transcriptional terminator. World J Microbiol Biotechnol 2023; 39:246. [PMID: 37420160 DOI: 10.1007/s11274-023-03682-5] [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: 10/22/2022] [Accepted: 06/16/2023] [Indexed: 07/09/2023]
Abstract
The methylotrophic yeast Komagataella phaffii (syn. Pichia pastoris) is a widely used host for extracellularly producing heterologous proteins via an expression cassette integrated into the yeast genome. A strong promoter in the expression cassette is not always the most favorable choice for heterologous protein production, especially if the correct folding of the protein and/or post-translational processing is the limiting step. The transcriptional terminator is another regulatory element in the expression cassette that can modify the expression levels of the heterologous gene. In this work, we identified and functionally characterized the promoter (P1033) and transcriptional terminator (T1033) of a constitutive gene (i.e., the 1033 gene) with a weak non-methanol-dependent transcriptional activity. We constructed two K. phaffii strains with two combinations of the regulatory DNA elements from the 1033 and AOX1 genes (i.e., P1033-TAOX1 and P1033-T1033 pairs) and evaluated the impact of the regulatory element combinations on the transcript levels of the heterologous gene and endogenous 1033 and GAPDH genes in cells grown in glucose or glycerol, and on the extracellular product/biomass yield. The results indicate that the P1033 has a 2-3% transcriptional activity of the GAP promoter and it is tunable by cell growth and the carbon source. The combinations of the regulatory elements rendered different transcriptional activity of the heterologous and endogenous genes that were dependent on the carbon source. The promoter-terminator pair and the carbon source affected the heterologous gene translation and/or protein secretion pathway. Moreover, low heterologous gene-transcript levels along with glycerol cultures increased translation and/or protein secretion.
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Affiliation(s)
- Yanelis Robainas-Del-Pino
- Facultad de Ciencias Biológicas, Instituto de Biotecnología, Universidad Autónoma de Nuevo León UANL, Av. Universidad S/N Col. Ciudad Universitaria, 66455, San Nicolás de los Garza, Nuevo León, Mexico
| | - José María Viader-Salvadó
- Facultad de Ciencias Biológicas, Instituto de Biotecnología, Universidad Autónoma de Nuevo León UANL, Av. Universidad S/N Col. Ciudad Universitaria, 66455, San Nicolás de los Garza, Nuevo León, Mexico.
| | - Ana Lucía Herrera-Estala
- Facultad de Ciencias Biológicas, Instituto de Biotecnología, Universidad Autónoma de Nuevo León UANL, Av. Universidad S/N Col. Ciudad Universitaria, 66455, San Nicolás de los Garza, Nuevo León, Mexico
| | - Martha Guerrero-Olazarán
- Facultad de Ciencias Biológicas, Instituto de Biotecnología, Universidad Autónoma de Nuevo León UANL, Av. Universidad S/N Col. Ciudad Universitaria, 66455, San Nicolás de los Garza, Nuevo León, Mexico.
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15
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Zhu SB, Jiang QH, Chen ZG, Zhou X, Jin YT, Deng Z, Guo FB. Mslar: Microbial synthetic lethal and rescue database. PLoS Comput Biol 2023; 19:e1011218. [PMID: 37289843 DOI: 10.1371/journal.pcbi.1011218] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 05/26/2023] [Indexed: 06/10/2023] Open
Abstract
Synthetic lethality (SL) occurs when mutations in two genes together lead to cell or organism death, while a single mutation in either gene does not have a significant impact. This concept can also be extended to three or more genes for SL. Computational and experimental methods have been developed to predict and verify SL gene pairs, especially for yeast and Escherichia coli. However, there is currently a lack of a specialized platform to collect microbial SL gene pairs. Therefore, we designed a synthetic interaction database for microbial genetics that collects 13,313 SL and 2,994 Synthetic Rescue (SR) gene pairs that are reported in the literature, as well as 86,981 putative SL pairs got through homologous transfer method in 281 bacterial genomes. Our database website provides multiple functions such as search, browse, visualization, and Blast. Based on the SL interaction data in the S. cerevisiae, we review the issue of duplications' essentiality and observed that the duplicated genes and singletons have a similar ratio of being essential when we consider both individual and SL. The Microbial Synthetic Lethal and Rescue Database (Mslar) is expected to be a useful reference resource for researchers interested in the SL and SR genes of microorganisms. Mslar is open freely to everyone and available on the web at http://guolab.whu.edu.cn/Mslar/.
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Affiliation(s)
- Sen-Bin Zhu
- School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Qian-Hu Jiang
- School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Zhi-Guo Chen
- School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Xiang Zhou
- School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Yan-Ting Jin
- School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Feng-Biao Guo
- Department of Respiratory and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
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16
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Bryant P. Deep learning for protein complex structure prediction. Curr Opin Struct Biol 2023; 79:102529. [PMID: 36731337 DOI: 10.1016/j.sbi.2023.102529] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 12/10/2022] [Accepted: 12/20/2022] [Indexed: 02/04/2023]
Abstract
Recent developments in the structure prediction of protein complexes have resulted in accuracies rivalling experimental methods in many cases. The high accuracy is mainly observed in dimeric complexes and other problems such as protein disorder and predicting the structure of host-pathogen interactions remain. This review highlights the foundation for current accurate structure prediction of protein complexes and possible ways to address the remaining limitations.
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Affiliation(s)
- Patrick Bryant
- Science for Life Laboratory, 172 21 Solna, Sweden; Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden.
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17
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Fulton JE, Drobik-Czwarno W, Lund AR, Schmidt CJ, Taylor RL. CD99 and the Chicken Alloantigen D Blood System. Genes (Basel) 2023; 14:402. [PMID: 36833329 PMCID: PMC9957549 DOI: 10.3390/genes14020402] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/09/2022] [Accepted: 01/28/2023] [Indexed: 02/05/2023] Open
Abstract
The chicken D blood system is one of 13 alloantigen systems found on chicken red blood cells. Classical recombinant studies located the D blood system on chicken chromosome 1, but the candidate gene was unknown. Multiple resources were utilized to identify the chicken D system candidate gene, including genome sequence information from both research and elite egg production lines for which D system alloantigen alleles were reported, and DNA from both pedigree and non-pedigree samples with known D alleles. Genome-wide association analyses using a 600 K or a 54 K SNP chip plus DNA from independent samples identified a strong peak on chicken chromosome 1 at 125-131 Mb (GRCg6a). Cell surface expression and the presence of exonic non-synonymous SNP were used to identify the candidate gene. The chicken CD99 gene showed the co-segregation of SNP-defined haplotypes and serologically defined D blood system alleles. The CD99 protein mediates multiple cellular processes including leukocyte migration, T-cell adhesion, and transmembrane protein transport, affecting peripheral immune responses. The corresponding human gene is found syntenic to the pseudoautosomal region 1 of human X and Y chromosomes. Phylogenetic analyses show that CD99 has a paralog, XG, that arose by duplication in the last common ancestor of the amniotes.
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Affiliation(s)
| | - Wiola Drobik-Czwarno
- Department of Animal Genetics and Conservation, Institute of Animal Science, Warsaw University of Life Sciences, 02-787 Warsaw, Poland
| | | | - Carl J. Schmidt
- Department of Animal and Food Science, University of Delaware, Newark, DE 19716, USA
| | - Robert L. Taylor
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, USA
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18
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Chagas MDS, Medeiros F, dos Santos MT, de Menezes MA, Carvalho-Assef APD, da Silva FAB. An updated gene regulatory network reconstruction of multidrug-resistant Pseudomonas aeruginosa CCBH4851. Mem Inst Oswaldo Cruz 2022; 117:e220111. [PMID: 36259790 PMCID: PMC9565603 DOI: 10.1590/0074-02760220111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 09/09/2022] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Healthcare-associated infections due to multidrug-resistant (MDR) bacteria such as Pseudomonas aeruginosa are significant public health issues worldwide. A system biology approach can help understand bacterial behaviour and provide novel ways to identify potential therapeutic targets and develop new drugs. Gene regulatory networks (GRN) are examples of in silico representation of interaction between regulatory genes and their targets. OBJECTIVES In this work, we update the MDR P. aeruginosa CCBH4851 GRN reconstruction and analyse and discuss its structural properties. METHODS We based this study on the gene orthology inference methodology using the reciprocal best hit method. The P. aeruginosa CCBH4851 genome and GRN, published in 2019, and the P. aeruginosa PAO1 GRN, published in 2020, were used for this update reconstruction process. FINDINGS Our result is a GRN with a greater number of regulatory genes, target genes, and interactions compared to the previous networks, and its structural properties are consistent with the complexity of biological networks and the biological features of P. aeruginosa. MAIN CONCLUSIONS Here, we present the largest and most complete version of P. aeruginosa GRN published to this date, to the best of our knowledge.
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Affiliation(s)
- Márcia da Silva Chagas
- Fundação Oswaldo Cruz-Fiocruz, Programa de Computação Científica, Rio de Janeiro, RJ, Brasil,+ Corresponding authors: /
| | - Fernando Medeiros
- Fundação Oswaldo Cruz-Fiocruz, Instituto Nacional de Infectologia, Laboratório de Pesquisa Clínica em Doenças Febris Agudas, Rio de Janeiro, RJ, Brasil
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19
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Monzon V, Paysan-Lafosse T, Wood V, Bateman A. Reciprocal best structure hits: using AlphaFold models to discover distant homologues. BIOINFORMATICS ADVANCES 2022; 2:vbac072. [PMID: 36408459 PMCID: PMC9666668 DOI: 10.1093/bioadv/vbac072] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 09/16/2022] [Accepted: 10/05/2022] [Indexed: 11/17/2022]
Abstract
Motivation The conventional methods to detect homologous protein pairs use the comparison of protein sequences. But the sequences of two homologous proteins may diverge significantly and consequently may be undetectable by standard approaches. The release of the AlphaFold 2.0 software enables the prediction of highly accurate protein structures and opens many opportunities to advance our understanding of protein functions, including the detection of homologous protein structure pairs. Results In this proof-of-concept work, we search for the closest homologous protein pairs using the structure models of five model organisms from the AlphaFold database. We compare the results with homologous protein pairs detected by their sequence similarity and show that the structural matching approach finds a similar set of results. In addition, we detect potential novel homologs solely with the structural matching approach, which can help to understand the function of uncharacterized proteins and make previously overlooked connections between well-characterized proteins. We also observe limitations of our implementation of the structure-based approach, particularly when handling highly disordered proteins or short protein structures. Our work shows that high accuracy protein structure models can be used to discover homologous protein pairs, and we expose areas for improvement of this structural matching approach. Availability and Implementation Information to the discovered homologous protein pairs can be found at the following URL: https://doi.org/10.17863/CAM.87873. The code can be accessed here: https://github.com/VivianMonzon/Reciprocal_Best_Structure_Hits. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
- Vivian Monzon
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB21 4HH, UK
| | - Typhaine Paysan-Lafosse
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB21 4HH, UK
| | - Valerie Wood
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Alex Bateman
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB21 4HH, UK
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20
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Su X, Liu T, Liu YP, Harris AJ, Chen JY. Adaptive radiation in Orinus, an endemic alpine grass of the Qinghai-Tibet Plateau, based on comparative transcriptomic analysis. JOURNAL OF PLANT PHYSIOLOGY 2022; 277:153786. [PMID: 35963042 DOI: 10.1016/j.jplph.2022.153786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/20/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
The species of Orinus (Poaceae) are important alpine plants with a variety of phenotypic traits and potential usages in molecular breeding toward drought-tolerant forage crops. However, the genetic basis of evolutionary adaption and diversification in the genus is still unclear. In the present study, we obtained transcriptomes for the two most divergent species, O. thoroldii and O. kokonoricus, using the Illumina platform and de novo assembly. In total, we generated 23,029 and 24,086 unigenes with N50 values of 1188 and 1203 for O. thoroldii and O. kokonoricus respectively, and identified 19,005 pairs of putative orthologs between the two species of Orinus. For these orthologs, estimations of non-synonymous/synonymous substitution rate ratios indicated that 568 pairs may be under strongly positive selection (Ka/Ks > 1), and Gene Ontogeny (GO) enrichment analysis revealed that significantly enriched pathways were in DNA repair and resistance to abiotic stress. Meanwhile, the divergence times of species between O. thoroldii and O. kokonoricus occurred 3.2 million years ago (Mya), and the recent evolutionary branch is an allotetraploid species, Cleistogenes songorica. We also detected a Ks peak of ∼0.60 for Orinus. Additionally, we identified 188 pairs of differentially expressed genes (DEGs) between the two species of Orinus, which were significantly enrich in stress resistance and lateral root development. Thus, we considered that the species diversification and evolutionary adaption of this genus was initiated by environmental selection, followed by phenotypic differentiation, finally leading to niche separation in the Qinghai-Tibet Plateau.
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Affiliation(s)
- Xu Su
- School of Life Sciences, Qinghai Normal University, Xining, 810008, China; Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, 810016, China; Key Laboratory of Medicinal Animal and Plant Resources of the Qinghai-Tibet Plateau in Qinghai Province, Qinghai Normal University, Xining, 810008, China; Key Laboratory of Land Surface Processes and Ecological Conservation of the Qinghai-Tibet Plateau, The Ministry of Education, Qinghai Normal University, Xining, 810008, China
| | - Tao Liu
- School of Life Sciences, Qinghai Normal University, Xining, 810008, China; School of Geographical Science, Qinghai Normal University, Xining, 810008, China
| | - Yu Ping Liu
- School of Life Sciences, Qinghai Normal University, Xining, 810008, China; Key Laboratory of Medicinal Animal and Plant Resources of the Qinghai-Tibet Plateau in Qinghai Province, Qinghai Normal University, Xining, 810008, China.
| | - A J Harris
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
| | - Jin Yuan Chen
- School of Life Sciences, Qinghai Normal University, Xining, 810008, China; Key Laboratory of Medicinal Animal and Plant Resources of the Qinghai-Tibet Plateau in Qinghai Province, Qinghai Normal University, Xining, 810008, China
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21
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Escorcia-Rodríguez JM, Esposito M, Freyre-González JA, Moreno-Hagelsieb G. Non-synonymous to synonymous substitutions suggest that orthologs tend to keep their functions, while paralogs are a source of functional novelty. PeerJ 2022; 10:e13843. [PMID: 36065404 PMCID: PMC9440661 DOI: 10.7717/peerj.13843] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 07/14/2022] [Indexed: 01/18/2023] Open
Abstract
Orthologs separate after lineages split from each other and paralogs after gene duplications. Thus, orthologs are expected to remain more functionally coherent across lineages, while paralogs have been proposed as a source of new functions. Because protein functional divergence follows from non-synonymous substitutions, we performed an analysis based on the ratio of non-synonymous to synonymous substitutions (dN/dS), as proxy for functional divergence. We used five working definitions of orthology, including reciprocal best hits (RBH), among other definitions based on network analyses and clustering. The results showed that orthologs, by all definitions tested, had values of dN/dS noticeably lower than those of paralogs, suggesting that orthologs generally tend to be more functionally stable than paralogs. The differences in dN/dS ratios remained suggesting the functional stability of orthologs after eliminating gene comparisons with potential problems, such as genes with high codon usage biases, low coverage of either of the aligned sequences, or sequences with very high similarities. Separation by percent identity of the encoded proteins showed that the differences between the dN/dS ratios of orthologs and paralogs were more evident at high sequence identity, less so as identity dropped. The last results suggest that the differences between dN/dS ratios were partially related to differences in protein identity. However, they also suggested that paralogs undergo functional divergence relatively early after duplication. Our analyses indicate that choosing orthologs as probably functionally coherent remains the right approach in comparative genomics.
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Affiliation(s)
- Juan M. Escorcia-Rodríguez
- Regulatory Systems Biology Research Group, Program of Systems Biology, Center for Genomic Sciences, Universidad Nacional Autonóma de México, Cuernavaca, Morelos, México
| | - Mario Esposito
- Department of Biology, Wilfrid Laurier University, Waterloo, Canada
| | - Julio A. Freyre-González
- Regulatory Systems Biology Research Group, Program of Systems Biology, Center for Genomic Sciences, Universidad Nacional Autonóma de México, Cuernavaca, Morelos, México
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22
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Rodriguez-Valbuena H, Gonzalez-Muñoz A, Cadavid LF. Multiple Alr genes exhibit allorecognition-associated variation in the colonial cnidarian Hydractinia. Immunogenetics 2022; 74:559-581. [PMID: 35761101 DOI: 10.1007/s00251-022-01268-3] [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: 03/26/2022] [Accepted: 06/19/2022] [Indexed: 11/25/2022]
Abstract
The genetics of allorecognition has been studied extensively in inbred lines of Hydractinia symbiolongicarpus, in which genetic control is attributed mainly to the highly polymorphic loci allorecognition 1 (Alr1) and allorecognition 2 (Alr2), located within the Allorecognition Complex (ARC). While allelic variation at Alr1 and Alr2 can predict the phenotypes in inbred lines, these two loci do not entirely predict the allorecognition phenotypes in wild-type colonies and their progeny, suggesting the presence of additional uncharacterized genes that are involved in the regulation of allorecognition in this species. Comparative genomics analyses were used to identify coding sequence differences from assembled chromosomal intervals of the ARC and from genomic scaffold sequences between two incompatible H. symbiolongicarpus siblings from a backcross population. New immunoglobulin superfamily (Igsf) genes are reported for the ARC, where five of these genes are closely related to the Alr1 and Alr2 genes, suggesting the presence of multiple Alr-like genes within this complex. Complementary DNA sequence evidence revealed that the allelic polymorphism of eight Igsf genes is associated with allorecognition phenotypes in a backcross population of H. symbiolongicarpus, yet that association was not found between parental colonies and their offspring. Alternative splicing was found as a mechanism that contributes to the variability of these genes by changing putative activating receptors to inhibitory receptors or generating secreted isoforms of allorecognition proteins. Our findings demonstrate that allorecognition in H. symbiolongicarpus is a multigenic phenomenon controlled by genetic variation in at least eight genes in the ARC complex.
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Affiliation(s)
- Henry Rodriguez-Valbuena
- Instituto de Genética, Universidad Nacional de Colombia, Bogotá, Colombia.
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA, USA.
| | - Andrea Gonzalez-Muñoz
- Instituto de Genética, Universidad Nacional de Colombia, Bogotá, Colombia
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Luis F Cadavid
- Instituto de Genética, Universidad Nacional de Colombia, Bogotá, Colombia
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23
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Solmi L, Rosli HG, Pombo MA, Stalder S, Rossi FR, Romero FM, Ruiz OA, Gárriz A. Inferring the Significance of the Polyamine Metabolism in the Phytopathogenic Bacteria Pseudomonas syringae: A Meta-Analysis Approach. Front Microbiol 2022; 13:893626. [PMID: 35602047 PMCID: PMC9120772 DOI: 10.3389/fmicb.2022.893626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 04/13/2022] [Indexed: 11/21/2022] Open
Abstract
To succeed in plant invasion, phytopathogenic bacteria rely on virulence mechanisms to subvert plant immunity and create favorable conditions for growth. This process requires a precise regulation in the production of important proteins and metabolites. Among them, the family of compounds known as polyamines have attracted considerable attention as they are involved in important cellular processes, but it is not known yet how phytopathogenic bacteria regulate polyamine homeostasis in the plant environment. In the present study, we performed a meta-analysis of publicly available transcriptomic data from experiments conducted on bacteria to begin delving into this topic and better understand the regulation of polyamine metabolism and its links to pathogenicity. We focused our research on Pseudomonas syringae, an important phytopathogen that causes disease in many economically valuable plant species. Our analysis discovered that polyamine synthesis, as well as general gene expression activation and energy production are induced in the early stages of the disease. On the contrary, synthesis of these compounds is inhibited whereas its transport is upregulated later in the process, which correlates with the induction of virulence genes and the metabolism of nitrogen and carboxylic acids. We also found that activation of plant defense mechanisms affects bacterial polyamine synthesis to some extent, which could reduce bacterial cell fitness in the plant environment. Furthermore, data suggest that a proper bacterial response to oxidative conditions requires a decrease in polyamine production. The implications of these findings are discussed.
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Affiliation(s)
- Leandro Solmi
- Laboratorio de Estrés Biótico y Abiótico en Plantas-Instituto Tecnológico de Chascomús (INTECh), Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad Nacional de General San Martín (CONICET-UNSAM), Chascomús, Argentina
| | - Hernán G. Rosli
- Laboratorio de Interacciones Planta Patógeno-Instituto de Fisiología Vegetal (INFIVE), Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad Nacional de La Plata (CONICET-UNLP), La Plata, Argentina
| | - Marina A. Pombo
- Laboratorio de Interacciones Planta Patógeno-Instituto de Fisiología Vegetal (INFIVE), Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad Nacional de La Plata (CONICET-UNLP), La Plata, Argentina
| | - Santiago Stalder
- Laboratorio de Estrés Biótico y Abiótico en Plantas-Instituto Tecnológico de Chascomús (INTECh), Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad Nacional de General San Martín (CONICET-UNSAM), Chascomús, Argentina
| | - Franco R. Rossi
- Laboratorio de Estrés Biótico y Abiótico en Plantas-Instituto Tecnológico de Chascomús (INTECh), Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad Nacional de General San Martín (CONICET-UNSAM), Chascomús, Argentina
| | - Fernando M. Romero
- Laboratorio de Estrés Biótico y Abiótico en Plantas-Instituto Tecnológico de Chascomús (INTECh), Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad Nacional de General San Martín (CONICET-UNSAM), Chascomús, Argentina
| | - Oscar A. Ruiz
- Laboratorio de Estrés Biótico y Abiótico en Plantas-Instituto Tecnológico de Chascomús (INTECh), Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad Nacional de General San Martín (CONICET-UNSAM), Chascomús, Argentina
| | - Andrés Gárriz
- Laboratorio de Estrés Biótico y Abiótico en Plantas-Instituto Tecnológico de Chascomús (INTECh), Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad Nacional de General San Martín (CONICET-UNSAM), Chascomús, Argentina
- *Correspondence: Andrés Gárriz,
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Keller LJ, Lakemeyer M, Bogyo M. Integration of bioinformatic and chemoproteomic tools for the study of enzyme conservation in closely related bacterial species. Methods Enzymol 2022; 664:1-22. [PMID: 35331369 DOI: 10.1016/bs.mie.2021.11.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Activity-based protein profiling (ABPP) is a commonly utilized technique to globally characterize the endogenous activity of multiple enzymes within a related family. While it has been used extensively to identify enzymes that are differentially active across various mammalian tissues, recent efforts have expanded this technique to studying bacteria. As ABPP is applied to diverse sets of bacterial strains found in microbial communities, there is also an increasing need for robust tools for assessing the conservation of enzymes across closely related bacterial species and strains. In this chapter, we detail the integration of gel-based ABPP with basic bioinformatic tools to enable the analysis of enzyme activity, distribution, and homology. We use as an example the family of serine hydrolases identified in the skin commensal bacterium Staphylococcus epidermidis.
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Affiliation(s)
- Laura J Keller
- Department of Chemical & Systems Biology, Stanford University, Stanford, CA, United States
| | - Markus Lakemeyer
- Department of Pathology, Stanford University, Stanford, CA, United States
| | - Matthew Bogyo
- Department of Pathology, Stanford University, Stanford, CA, United States; Department of Microbiology and Immunology, Stanford University, Stanford, CA, United States.
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Farhat S, Bonnivard E, Pales Espinosa E, Tanguy A, Boutet I, Guiglielmoni N, Flot JF, Allam B. Comparative analysis of the Mercenaria mercenaria genome provides insights into the diversity of transposable elements and immune molecules in bivalve mollusks. BMC Genomics 2022; 23:192. [PMID: 35260071 PMCID: PMC8905726 DOI: 10.1186/s12864-021-08262-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/15/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND The hard clam Mercenaria mercenaria is a major marine resource along the Atlantic coasts of North America and has been introduced to other continents for resource restoration or aquaculture activities. Significant mortality events have been reported in the species throughout its native range as a result of diseases (microbial infections, leukemia) and acute environmental stress. In this context, the characterization of the hard clam genome can provide highly needed resources to enable basic (e.g., oncogenesis and cancer transmission, adaptation biology) and applied (clam stock enhancement, genomic selection) sciences. RESULTS Using a combination of long and short-read sequencing technologies, a 1.86 Gb chromosome-level assembly of the clam genome was generated. The assembly was scaffolded into 19 chromosomes, with an N50 of 83 Mb. Genome annotation yielded 34,728 predicted protein-coding genes, markedly more than the few other members of the Venerida sequenced so far, with coding regions representing only 2% of the assembly. Indeed, more than half of the genome is composed of repeated elements, including transposable elements. Major chromosome rearrangements were detected between this assembly and another recent assembly derived from a genetically segregated clam stock. Comparative analysis of the clam genome allowed the identification of a marked diversification in immune-related proteins, particularly extensive tandem duplications and expansions in tumor necrosis factors (TNFs) and C1q domain-containing proteins, some of which were previously shown to play a role in clam interactions with infectious microbes. The study also generated a comparative repertoire highlighting the diversity and, in some instances, the specificity of LTR-retrotransposons elements, particularly Steamer elements in bivalves. CONCLUSIONS The diversity of immune molecules in M. mercenaria may allow this species to cope with varying and complex microbial and environmental landscapes. The repertoire of transposable elements identified in this study, particularly Steamer elements, should be a prime target for the investigation of cancer cell development and transmission among bivalve mollusks.
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Affiliation(s)
- Sarah Farhat
- Marine Animal Disease Laboratory, School of Marine and Atmospheric Sciences, 100 Nicolls Road, Stony Brook University, Stony Brook, NY, 11794-5000, USA
| | - Eric Bonnivard
- Sorbonne Université, CNRS, UMR 7144 AD2M, Station Biologique de Roscoff, Place Georges Teissier, 29688, Roscoff, France
| | - Emmanuelle Pales Espinosa
- Marine Animal Disease Laboratory, School of Marine and Atmospheric Sciences, 100 Nicolls Road, Stony Brook University, Stony Brook, NY, 11794-5000, USA
| | - Arnaud Tanguy
- Sorbonne Université, CNRS, UMR 7144 AD2M, Station Biologique de Roscoff, Place Georges Teissier, 29688, Roscoff, France
| | - Isabelle Boutet
- Sorbonne Université, CNRS, UMR 7144 AD2M, Station Biologique de Roscoff, Place Georges Teissier, 29688, Roscoff, France
| | - Nadège Guiglielmoni
- Université libre de Bruxelles (ULB), Evolutionary Biology & Ecology, Avenue F.D. Roosevelt 50, B-1050, Brussels, Belgium
| | - Jean-François Flot
- Université libre de Bruxelles (ULB), Evolutionary Biology & Ecology, Avenue F.D. Roosevelt 50, B-1050, Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels - (IB)2, B-1050, Brussels, Belgium
| | - Bassem Allam
- Marine Animal Disease Laboratory, School of Marine and Atmospheric Sciences, 100 Nicolls Road, Stony Brook University, Stony Brook, NY, 11794-5000, USA.
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Hahm C, Chung HS, Lee M. Whole-genome sequencing for the characterization of resistance mechanisms and epidemiology of colistin-resistant Acinetobacter baumannii. PLoS One 2022; 17:e0264335. [PMID: 35245298 PMCID: PMC8896714 DOI: 10.1371/journal.pone.0264335] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 02/08/2022] [Indexed: 11/18/2022] Open
Abstract
Background Multidrug-resistant Acinetobacter baumannii is an important causal pathogen of healthcare-associated infections, and colistin-resistant strains have recently emerged owing to the increased use of colistin. Using next-generation sequencing (NGS), a single whole-genome sequencing (WGS) protocol can identify and type pathogens, analyze genetic relationships among different pathogens, predict pathogenic transmissions, and detect antibiotic resistance genes. However, only a few studies have applied NGS in studying the resistance mechanism and epidemiology of colistin-resistant A. baumannii. This study aimed to elucidate the resistance mechanism of colistin-resistant A. baumannii and analyze its molecular epidemiology through WGS. Materials and methods The subjects in this study were patients who visited a university hospital between 2014 and 2018. Thirty colistin-resistant strains with high minimum inhibitory concentrations were selected from various patient samples, and WGS was performed. Comparative genomic analysis was performed for the 27 colistin-resistant A. baumannii strains using a colistin-susceptible strain as the reference genome. Results The WGS analysis found no mutation for lpxA, lpxC, lpx D, pmrA, pmrB, and mcr1, the genes known to be associated with colistin resistance. Fifty-seven coding sequences (CDS) showed differences; they included 13 CDS with known names and functions that contained 21 genes. From the whole-genome multi-locus sequence typing (wgMLST) and single nucleotide polymorphism (SNP) analyses, two major clusters were found for the colistin-resistant A. baumannii strains. However, no differences were observed by the time of detection for each cluster, the samples, the pattern of antibiotic resistance, or the patient characteristics. In the conventional MLST following the Oxford scheme, the typing result showed ST1809, ST451, ST191, ST1837, and ST369 in the global clone 2 (GC2), without any relation with the results of wgMLST and SNP analyses. Conclusion Based on the findings of the resistance gene analysis through WGS and comparative genomic analysis, the potential genes associated with colistin-resistance or CDS were examined. Furthermore, the analysis of molecular epidemiology through WGS regarding colistin-resistant A. baumannii may prove helpful in preventing infection by multidrug-resistant bacteria and controlling healthcare-associated infections.
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Affiliation(s)
- Chorong Hahm
- Department of Laboratory Medicine, College of Medicine, Ewha Womans University, Seoul, Korea
- Department of Laboratory Medicine, Eone Laboratories, Incheon, Korea
| | - Hae-Sun Chung
- Department of Laboratory Medicine, College of Medicine, Ewha Womans University, Seoul, Korea
- EWHA Education and Research Center for Infection, College of Medicine, Ewha Womans University, Seoul, Korea
| | - Miae Lee
- Department of Laboratory Medicine, College of Medicine, Ewha Womans University, Seoul, Korea
- EWHA Education and Research Center for Infection, College of Medicine, Ewha Womans University, Seoul, Korea
- * E-mail:
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Vazquez JM, Pena MT, Muhammad B, Kraft M, Adams LB, Lynch VJ. Parallel evolution of reduced cancer risk and tumor suppressor duplications in Xenarthra. eLife 2022; 11:82558. [PMID: 36480266 PMCID: PMC9810328 DOI: 10.7554/elife.82558] [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: 08/09/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
The risk of developing cancer is correlated with body size and lifespan within species, but there is no correlation between cancer and either body size or lifespan between species indicating that large, long-lived species have evolved enhanced cancer protection mechanisms. Previously we showed that several large bodied Afrotherian lineages evolved reduced intrinsic cancer risk, particularly elephants and their extinct relatives (Proboscideans), coincident with pervasive duplication of tumor suppressor genes (Vazquez and Lynch, 2021). Unexpectedly, we also found that Xenarthrans (sloths, armadillos, and anteaters) evolved very low intrinsic cancer risk. Here, we show that: (1) several Xenarthran lineages independently evolved large bodies, long lifespans, and reduced intrinsic cancer risk; (2) the reduced cancer risk in the stem lineages of Xenarthra and Pilosa coincided with bursts of tumor suppressor gene duplications; (3) cells from sloths proliferate extremely slowly while Xenarthran cells induce apoptosis at very low doses of DNA damaging agents; and (4) the prevalence of cancer is extremely low Xenarthrans, and cancer is nearly absent from armadillos. These data implicate the duplication of tumor suppressor genes in the evolution of remarkably large body sizes and decreased cancer risk in Xenarthrans and suggest they are a remarkably cancer-resistant group of mammals.
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Affiliation(s)
- Juan Manuel Vazquez
- Department of Integrative Biology, Valley Life Sciences, University of California, BerkeleyBerkeleyUnited States
| | - Maria T Pena
- United States Department of Health and Human Services, Health Resources and Services Administration, Health Systems Bureau, National Hansen's Disease ProgramBaton RougeUnited States
| | - Baaqeyah Muhammad
- Department of Biological Sciences, University at Buffalo, SUNYBuffaloUnited States
| | - Morgan Kraft
- Department of Biological Sciences, University at Buffalo, SUNYBuffaloUnited States
| | - Linda B Adams
- United States Department of Health and Human Services, Health Resources and Services Administration, Health Systems Bureau, National Hansen's Disease ProgramBaton RougeUnited States
| | - Vincent J Lynch
- Department of Biological Sciences, University at Buffalo, SUNYBuffaloUnited States
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Sánchez AL, Lafond M. Colorful orthology clustering in bounded-degree similarity graphs. J Bioinform Comput Biol 2021; 19:2140010. [PMID: 34775924 DOI: 10.1142/s0219720021400102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Clustering genes in similarity graphs is a popular approach for orthology prediction. Most algorithms group genes without considering their species, which results in clusters that contain several paralogous genes. Moreover, clustering is known to be problematic when in-paralogs arise from ancient duplications. Recently, we proposed a two-step process that avoids these problems. First, we infer clusters of only orthologs (i.e. with only genes from distinct species), and second, we infer the missing inter-cluster orthologs. In this paper, we focus on the first step, which leads to a problem we call Colorful Clustering. In general, this is as hard as classical clustering. However, in similarity graphs, the number of species is usually small, as well as the neighborhood size of genes in other species. We therefore study the problem of clustering in which the number of colors is bounded by [Formula: see text], and each gene has at most [Formula: see text] neighbors in another species. We show that the well-known cluster editing formulation remains NP-hard even when [Formula: see text] and [Formula: see text]. We then propose a fixed-parameter algorithm in [Formula: see text] to find the single best cluster in the graph. We implemented this algorithm and included it in the aforementioned two-step approach. Experiments on simulated data show that this approach performs favorably to applying only an unconstrained clustering step.
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Affiliation(s)
- Alitzel López Sánchez
- Computer Science Department, Université de Sherbrooke, 2500 Boulevard de l'Université, Sherbrooke, Québec J1K 2R1, Canada
| | - Manuel Lafond
- Computer Science Department, Université de Sherbrooke, 2500 Boulevard de l'Université, Sherbrooke, Québec J1K 2R1, Canada
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Shimada S, Nakai R, Aoki K, Kudoh S, Imura S, Shimoeda N, Ohno G, Watanabe K, Miyazaki Y, Ishii Y, Tateda K. Characterization of the First Cultured Psychrotolerant Representative of Legionella from Antarctica Reveals Its Unique Genome Structure. Microbiol Spectr 2021; 9:e0042421. [PMID: 34668737 PMCID: PMC8528123 DOI: 10.1128/spectrum.00424-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 09/14/2021] [Indexed: 11/20/2022] Open
Abstract
Culture-independent analysis shows that Legionella spp. inhabit a wide range of low-temperature environments, but to date, no psychrotolerant or psychrophilic strains have been reported. Here, we characterized the first cultivated psychrotolerant representative, designated strain TUM19329T, isolated from an Antarctic lake using a polyphasic approach and comparative genomic analysis. A genome-wide phylogenetic tree indicated that this strain was phylogenetically separate at the species level. Strain TUM19329T shared common physiological traits (e.g., Gram-negative, limited growth on buffered charcoal-yeast extract α-ketoglutarate [BCYEα] agar with l-cysteine requirements) with its relatives, but it also showed psychrotolerant growth properties (e.g., growth at 4°C to 25°C). Moreover, this strain altered its own cellular fatty acid composition to accumulate unsaturated fatty acid at a lower temperature, which may help maintain the cell membrane fluidity. Through comparative genomic analysis, we found that this strain possessed massive mobile genetic elements compared with other species, amounting to up to 17% of the total genes. The majority of the elements were the result of the spread of only a few insertion sequences (ISs), which were spread throughout the genome by a "copy-and-paste" mechanism. Furthermore, we found metabolic genes, such as fatty acid synthesis-related genes, acquired by horizontal gene transfer (HGT). The expansion of ISs and HGT events may play a major role in shaping the phenotype and physiology of this strain. On the basis of the features presented here, we propose a new species-Legionella antarctica sp. nov.-represented by strain TUM19329T (= GTC 22699T = NCTC 14581T). IMPORTANCE This study characterized a unique cultivated representative of the genus Legionella isolated from an Antarctic lake. This psychrotolerant strain had some common properties of known Legionella species but also displayed other characteristics, such as plasticity in fatty acid composition and an enrichment of mobile genes in the genome. These remarkable properties, as well as other factors, may contribute to cold hardiness, and this first cultivated cold-tolerant strain of the genus Legionella may serve as a model bacterium for further studies. It is worth noting that environmentally derived 16S rRNA gene phylotypes closely related to the strain characterized here have been detected from diverse environments outside Antarctica, suggesting a wide distribution of psychrotolerant Legionella bacteria. Our culture- and genome-based findings may accelerate the ongoing studies of the behavior and pathogenicity of Legionella spp., which have been monitored for many years in the context of public health.
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Affiliation(s)
- Sho Shimada
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
- Department of Respiratory Medicine, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Ryosuke Nakai
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Hokkaido, Japan
| | - Kotaro Aoki
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
| | - Sakae Kudoh
- National Institute of Polar Research, Research Organization of Information and Systems, Tokyo, Japan
- Department of Polar Science, The Graduate University for Advanced Studies, SOKENDAI, Tokyo, Japan
| | - Satoshi Imura
- National Institute of Polar Research, Research Organization of Information and Systems, Tokyo, Japan
- Department of Polar Science, The Graduate University for Advanced Studies, SOKENDAI, Tokyo, Japan
| | | | | | - Kentaro Watanabe
- National Institute of Polar Research, Research Organization of Information and Systems, Tokyo, Japan
| | - Yasunari Miyazaki
- Department of Respiratory Medicine, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Yoshikazu Ishii
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
| | - Kazuhiro Tateda
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
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Ballesteros HGF, Rosman AC, Carvalho TLG, Grativol C, Hemerly AS. Cell wall formation pathways are differentially regulated in sugarcane contrasting genotypes associated with endophytic diazotrophic bacteria. PLANTA 2021; 254:109. [PMID: 34705112 DOI: 10.1007/s00425-021-03768-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 10/20/2021] [Indexed: 06/13/2023]
Abstract
Differences in cell wall components between two BNF-contrasting sugarcane genotypes might result from genetic variations particular to the genotype and from the efficiency in diazotrophic bacteria association. Sugarcane is a plant of the grass family (Poaceae) that is highly cultivated in Brazil, as an important energy resource. Commercial sugarcane genotypes may be successfully associated with beneficial endophytic nitrogen-fixing bacteria, which can influence several plant metabolic pathways, such as cell division and growth, synthesis of hormones, and defense compounds. In this study, we investigated how diazotrophic bacteria associated with sugarcane plants could be involved in the regulation of cell wall formation pathways. A molecular and structural characterization of the cell wall was compared between two genotypes of sugarcane with contrasting rates of Biological Nitrogen Fixation (BNF): SP70-1143 (high BNF) and Chunee (low BNF). Differentially expressed transcripts were identified in transcriptomes generated from SP70-1143 and Chunee. Expression profiles of cellulose and lignin genes, which were more expressed in SP70-1134, and callose genes, which were more expressed in Chunee, were validated by RT-qPCR and microscopic analysis of cell wall components in tissue sections. A similar expression profile in both BNF-contrasting genotypes was observed in naturally colonized plants and in plants inoculated with G. diazotrophicus. Cell walls of the high BNF genotype have a greater cellulose content, which might contribute to increase biomass. In parallel, callose was concentrated in the vascular tissues of the low BNF genotype and could possibly represent a barrier for an efficient bacterial colonization and dissemination in sugarcane tissues. Our data show a correlation between the gene profiles identified in the BNF-contrasting genotypes and a successful association with endophytic diazotrophic bacteria.
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Affiliation(s)
- Helkin Giovani F Ballesteros
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-590, Brazil
| | - Aline C Rosman
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-590, Brazil
| | - Thais Louise G Carvalho
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-590, Brazil
- Departamento de Biologia, Pontifícia Universidade Católica do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Clicia Grativol
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-590, Brazil
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil
| | - Adriana Silva Hemerly
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-590, Brazil.
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Savini G, Scolari F, Ometto L, Rota-Stabelli O, Carraretto D, Gomulski LM, Gasperi G, Abd-Alla AMM, Aksoy S, Attardo GM, Malacrida AR. Viviparity and habitat restrictions may influence the evolution of male reproductive genes in tsetse fly (Glossina) species. BMC Biol 2021; 19:211. [PMID: 34556101 PMCID: PMC8461966 DOI: 10.1186/s12915-021-01148-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 09/06/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Glossina species (tsetse flies), the sole vectors of African trypanosomes, maintained along their long evolutionary history a unique reproductive strategy, adenotrophic viviparity. Viviparity reduces their reproductive rate and, as such, imposes strong selective pressures on males for reproductive success. These species live in sub-Saharan Africa, where the distributions of the main sub-genera Fusca, Morsitans, and Palpalis are restricted to forest, savannah, and riverine habitats, respectively. Here we aim at identifying the evolutionary patterns of the male reproductive genes of six species belonging to these three main sub-genera. We then interpreted the different patterns we found across the species in the light of viviparity and the specific habitat restrictions, which are known to shape reproductive behavior. RESULTS We used a comparative genomic approach to build consensus evolutionary trees that portray the selective pressure acting on the male reproductive genes in these lineages. Such trees reflect the long and divergent demographic history that led to an allopatric distribution of the Fusca, Morsitans, and Palpalis species groups. A dataset of over 1700 male reproductive genes remained conserved over the long evolutionary time scale (estimated at 26.7 million years) across the genomes of the six species. We suggest that this conservation may result from strong functional selective pressure on the male imposed by viviparity. It is noteworthy that more than half of these conserved genes are novel sequences that are unique to the Glossina genus and are candidates for selection in the different lineages. CONCLUSIONS Tsetse flies represent a model to interpret the evolution and differentiation of male reproductive biology under different, but complementary, perspectives. In the light of viviparity, we must take into account that these genes are constrained by a post-fertilization arena for genomic conflicts created by viviparity and absent in ovipositing species. This constraint implies a continuous antagonistic co-evolution between the parental genomes, thus accelerating inter-population post-zygotic isolation and, ultimately, favoring speciation. Ecological restrictions that affect reproductive behavior may further shape such antagonistic co-evolution.
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Affiliation(s)
- Grazia Savini
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Francesca Scolari
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
- Institute of Molecular Genetics IGM-CNR "Luigi Luca Cavalli-Sforza", Pavia, Italy
| | - Lino Ometto
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Omar Rota-Stabelli
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy
- Center Agriculture Food Environment (C3A), University of Trento, Trento, Italy
| | - Davide Carraretto
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Ludvik M Gomulski
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Giuliano Gasperi
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Adly M M Abd-Alla
- Insect Pest Control Laboratory, Joint FAO/IAEA Programme of Nuclear Techniques in Food & Agriculture, Vienna, Vienna, Austria.
| | - Serap Aksoy
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Geoffrey M Attardo
- Department of Entomology and Nematology, University of California, Davis, Davis, CA, USA
| | - Anna R Malacrida
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy.
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Osorio Zambrano MA, Castillo DA, Rodríguez Pérez L, Terán W. Cacao ( Theobroma cacao L.) Response to Water Stress: Physiological Characterization and Antioxidant Gene Expression Profiling in Commercial Clones. FRONTIERS IN PLANT SCIENCE 2021; 12:700855. [PMID: 34552605 PMCID: PMC8450537 DOI: 10.3389/fpls.2021.700855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 08/16/2021] [Indexed: 06/13/2023]
Abstract
The increase in events associated with drought constraints plant growth and crop performance. Cacao (Theobroma cacao L.) is sensitive to water deficit stress (DS), which limits productivity. The aim of this research was to characterise the response of seven (CCN51, FEAR5, ICS1, ICS60, ICS95, EET8, and TSH565) commercially important cacao clones to severe and temporal water deficit stress. Ten-month-old cacao trees were submitted to two treatments: well-watered and water-stressed until the leaf water potential (Ψ leaf) reached values between -3.0 and -3.5 MPa. The effects of hydric stress on water relations, gas exchange, photochemical activity, membrane integrity and oxidative stress-related gene expression were evaluated. All clones showed decreases in Ψ leaf, but TSH565 had a higher capacity to maintain water homeostasis in leaves. An initial response phase consisted of stomatal closure, a general mechanism to limit water loss: as a consequence, the photosynthetic rate dropped by approximately 98% on average. In some clones, the photosynthetic rate reached negative values at the maximum stress level, evidencing photorespiration and was confirmed by increased intracellular CO2. A second and photosynthetically limited phase was characterized by a drop in PSII quantum efficiency, which affected all clones. On average, all clones were able to recover after 4 days of rewatering. Water deficit triggered oxidative stress at the early phase, as evidenced by the upregulation of oxidative stress markers and genes encoding ROS scavenging enzymes. The effects of water deficit stress on energy metabolism were deduced given the upregulation of fermentative enzyme-coding genes. Altogether, our results suggest that the EET8 clone was the highest performing under water deficit while the ICS-60 clone was more susceptible to water stress. Importantly, the activation of the antioxidant system and PSII repair mechanism seem to play key roles in the observed differences in tolerance to water deficit stress among clones.
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Affiliation(s)
| | | | | | - Wilson Terán
- Plant and Crop Biology, Department of Biology, Pontificia Universidad Javeriana, Bogotá, Colombia
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Lakshmanan Mangalath D, Hassan Mohammed SA. Ligand Binding Domain of Estrogen Receptor Alpha Preserve a Conserved Structural Architecture Similar to Bacterial Taxis Receptors. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.681913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
It remains a mystery why estrogen hormone receptors (ERs), which are highly specific toward its endogenous hormones, are responsive to chemically distinct exogenous agents. Does it indicate that ERs are environmentally regulated? Here, we speculate that ERs would have some common structural features with prokaryotic taxis receptor responsive toward environmental signals. This study addresses the low specificity and high responsiveness of ERs toward chemically distinct exogenous substances, from an evolutionary point of view. Here, we compared the ligand binding domain (LBD) of ER alpha (α) with the LBDs of prokaryotic taxis receptors to check if LBDs share any structural similarity. Interestingly, a high degree of similarity in the domain structural fold architecture of ERα and bacterial taxis receptors was observed. The pharmacophore modeling focused on ligand molecules of both receptors suggest that these ligands share common pharmacophore features. The molecular docking studies suggest that the natural ligands of bacterial chemotaxis receptors exhibit strong interaction with human ER as well. Although phylogenetic analysis proved that these proteins are unrelated, they would have evolved independently, suggesting a possibility of convergent molecular evolution. Nevertheless, a remarkable sequence divergence was seen between these proteins even when they shared common domain structural folds and common ligand-based pharmacophore features, suggesting that the protein architecture remains conserved within the structure for a specific function irrespective of sequence identity.
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Legüe M, Aguila B, Calixto A. Interspecies RNA Interactome of Pathogen and Host in a Heritable Defensive Strategy. Front Microbiol 2021; 12:649858. [PMID: 34367078 PMCID: PMC8334366 DOI: 10.3389/fmicb.2021.649858] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 06/17/2021] [Indexed: 12/13/2022] Open
Abstract
Communication with bacteria deeply impacts the life history traits of their hosts. Through specific molecules and metabolites, bacteria can promote short- and long-term phenotypic and behavioral changes in the nematode Caenorhabditis elegans. The chronic exposure of C. elegans to pathogens promotes the adaptive behavior in the host’s progeny called pathogen-induced diapause formation (PIDF). PIDF is a pathogen avoidance strategy induced in the second generation of animals infected and can be recalled transgenerationally. This behavior requires the RNA interference machinery and specific nematode and bacteria small RNAs (sRNAs). In this work, we assume that RNAs from both species co-exist and can interact with each other. Under this principle, we explore the potential interspecies RNA interactions during PIDF-triggering conditions, using transcriptomic data from the holobiont. We study two transcriptomics datasets: first, the dual sRNA expression of Pseudomonas aeruginosa PAO1 and C. elegans in a transgenerational paradigm for six generations and second, the simultaneous expression of sRNAs and mRNA in intergenerational PIDF. We focus on those bacterial sRNAs that are systematically overexpressed in the intestines of animals compared with sRNAs expressed in host-naïve bacteria. We selected diverse in silico methods that represent putative mechanisms of RNA-mediated interspecies interaction. These interactions are as follows: heterologous perfect and incomplete pairing between bacterial RNA and host mRNA; sRNAs of similar sequence expressed in both species that could mimic each other; and known or predicted eukaryotic motifs present in bacterial transcripts. We conclude that a broad spectrum of tools can be applied for the identification of potential sRNA and mRNA targets of the interspecies RNA interaction that can be subsequently tested experimentally.
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Affiliation(s)
- Marcela Legüe
- Centro Interdisciplinario de Neurociencia de Valparaíso, Instituto de Neurociencia, Facultad de Ciencias, Universidad de Valparaíso, Valparaiso, Chile
| | - Blanca Aguila
- Centro Interdisciplinario de Neurociencia de Valparaíso, Instituto de Neurociencia, Facultad de Ciencias, Universidad de Valparaíso, Valparaiso, Chile.,Programa de Doctorado en Microbiología, Universidad de Chile, Santiago, Chile
| | - Andrea Calixto
- Centro Interdisciplinario de Neurociencia de Valparaíso, Instituto de Neurociencia, Facultad de Ciencias, Universidad de Valparaíso, Valparaiso, Chile
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35
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Cagirici HB, Budak H, Sen TZ. Genome-wide discovery of G-quadruplexes in barley. Sci Rep 2021; 11:7876. [PMID: 33846409 PMCID: PMC8041835 DOI: 10.1038/s41598-021-86838-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 03/19/2021] [Indexed: 12/04/2022] Open
Abstract
G-quadruplexes (G4s) are four-stranded nucleic acid structures with closely spaced guanine bases forming square planar G-quartets. Aberrant formation of G4 structures has been associated with genomic instability. However, most plant species are lacking comprehensive studies of G4 motifs. In this study, genome-wide identification of G4 motifs in barley was performed, followed by a comparison of genomic distribution and molecular functions to other monocot species, such as wheat, maize, and rice. Similar to the reports on human and some plants like wheat, G4 motifs peaked around the 5′ untranslated region (5′ UTR), the first coding domain sequence, and the first intron start sites on antisense strands. Our comparative analyses in human, Arabidopsis, maize, rice, and sorghum demonstrated that the peak points could be erroneously merged into a single peak when large window sizes are used. We also showed that the G4 distributions around genic regions are relatively similar in the species studied, except in the case of Arabidopsis. G4 containing genes in monocots showed conserved molecular functions for transcription initiation and hydrolase activity. Additionally, we provided examples of imperfect G4 motifs.
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Affiliation(s)
- H Busra Cagirici
- Crop Improvement and Genetics Research Unit, Western Regional Research Center, U.S. Department of Agriculture - Agricultural Research Service, 800 Buchanan St, Albany, CA, 94710, USA
| | - Hikmet Budak
- Montana BioAg Inc., Missoula, MT, USA.,Agrogen, LLC., Omaha, NE, USA
| | - Taner Z Sen
- Crop Improvement and Genetics Research Unit, Western Regional Research Center, U.S. Department of Agriculture - Agricultural Research Service, 800 Buchanan St, Albany, CA, 94710, USA.
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Lan J, Wang Z, Chen Z, Zhang L, Zhao J, Guan Q, Liao C, Liu N, Han Q. Identification of the Aedes aegypti nAChR gene family and molecular target of spinosad. PEST MANAGEMENT SCIENCE 2021; 77:1633-1641. [PMID: 33202106 DOI: 10.1002/ps.6183] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/18/2020] [Accepted: 11/17/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Spinosad is an insecticide with unique mode of action (MOA) of disrupting nicotinic acetylcholine receptor and is efficacious against many insect species. Mutations in the nicotinic acetylcholine receptor (nAChR) α6 subunit have been identified that are associated with levels of spinosad resistance, but the molecular characterization of the nAChR gene family and a causative association between nAChR α6 and resistance to spinosad in Aedes aegypti, a primary vector of many arboviruses, have not yet been reported. RESULTS In this study, we identified 10 candidate nAChR subunits in Ae. Aegypti, nAChRα1-α9 and nAChRβ1, showing similarly orthologous relationships with Anopheles gambiae. With the application of the CRISPR/Cas9 genome editing system, we introduced a 32-bp deletion at the 5' end of the Aaeα6 (Ae. aegypti nAChR α6) gene in a homozygous mutant strain (Aaeα6-KO). The mutation produced two successive pre-mature stop codons, resulting in loss of function in the target receptor. The Aaeα6-KO mutant strain exhibited a 320-fold level of resistance to spinosad compared with wildtype. A recessive mode of inheritance for spinosad resistance was found in the Aaeα6-KO strain. CONCLUSION CRISPR/Cas9 introduced truncated Aaeα6 receptor in Ae. aegypti resulted in an increased level of resistance to spinosad, suggesting that the conserved nAChR α6 subunit is the target for spinosad insecticide. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Jianqiang Lan
- Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, China
| | - Zihe Wang
- Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, China
| | - Zhaohui Chen
- Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, China
| | - Lei Zhang
- Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, China
| | - Jianguo Zhao
- Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, China
| | - Qingfeng Guan
- Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, China
| | - Chenghong Liao
- Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, China
| | - Nannan Liu
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
| | - Qian Han
- Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, China
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Baltussen TJH, Coolen JPM, Verweij PE, Dijksterhuis J, Melchers WJG. Identifying Conserved Generic Aspergillus spp. Co-Expressed Gene Modules Associated with Germination Using Cross-Platform and Cross-Species Transcriptomics. J Fungi (Basel) 2021; 7:270. [PMID: 33916245 PMCID: PMC8067318 DOI: 10.3390/jof7040270] [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: 02/22/2021] [Revised: 03/27/2021] [Accepted: 03/29/2021] [Indexed: 12/26/2022] Open
Abstract
Aspergillus spp. is an opportunistic human pathogen that may cause a spectrum of pulmonary diseases. In order to establish infection, inhaled conidia must germinate, whereby they break dormancy, start to swell, and initiate a highly polarized growth process. To identify critical biological processes during germination, we performed a cross-platform, cross-species comparative analysis of germinating A. fumigatus and A. niger conidia using transcriptional data from published RNA-Seq and Affymetrix studies. A consensus co-expression network analysis identified four gene modules associated with stages of germination. These modules showed numerous shared biological processes between A. niger and A. fumigatus during conidial germination. Specifically, the turquoise module was enriched with secondary metabolism, the black module was highly enriched with protein synthesis, the darkgreen module was enriched with protein fate, and the blue module was highly enriched with polarized growth. More specifically, enriched functional categories identified in the blue module were vesicle formation, vesicular transport, tubulin dependent transport, actin-dependent transport, exocytosis, and endocytosis. Genes important for these biological processes showed similar expression patterns in A. fumigatus and A. niger, therefore, they could be potential antifungal targets. Through cross-platform, cross-species comparative analysis, we were able to identify biologically meaningful modules shared by A. fumigatus and A. niger, which underscores the potential of this approach.
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Affiliation(s)
- Tim J. H. Baltussen
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (J.P.M.C.); (P.E.V.); (W.J.G.M.)
- Center of Expertise in Mycology Radboudumc/CWZ, 6532 SZ Nijmegen, The Netherlands
| | - Jordy P. M. Coolen
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (J.P.M.C.); (P.E.V.); (W.J.G.M.)
- Center of Expertise in Mycology Radboudumc/CWZ, 6532 SZ Nijmegen, The Netherlands
| | - Paul E. Verweij
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (J.P.M.C.); (P.E.V.); (W.J.G.M.)
- Center of Expertise in Mycology Radboudumc/CWZ, 6532 SZ Nijmegen, The Netherlands
| | - Jan Dijksterhuis
- Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands
| | - Willem J. G. Melchers
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (J.P.M.C.); (P.E.V.); (W.J.G.M.)
- Center of Expertise in Mycology Radboudumc/CWZ, 6532 SZ Nijmegen, The Netherlands
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38
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Fry MY, Saladi SM, Clemons WM. The STI1-domain is a flexible alpha-helical fold with a hydrophobic groove. Protein Sci 2021; 30:882-898. [PMID: 33620121 PMCID: PMC7980504 DOI: 10.1002/pro.4049] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 01/05/2023]
Abstract
STI1-domains are present in a variety of co-chaperone proteins and are required for the transfer of hydrophobic clients in various cellular processes. The domains were first identified in the yeast Sti1 protein where they were referred to as DP1 and DP2. Based on hidden Markov model searches, this domain had previously been found in other proteins including the mammalian co-chaperone SGTA, the DNA damage response protein Rad23, and the chloroplast import protein Tic40. Here, we refine the domain definition and carry out structure-based sequence alignment of STI1-domains showing conservation of five amphipathic helices. Upon examinations of these identified domains, we identify a preceding helix 0 and unifying sequence properties, determine new molecular models, and recognize that STI1-domains nearly always occur in pairs. The similarity at the sequence, structure, and molecular levels likely supports a unified functional role.
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Affiliation(s)
- Michelle Y. Fry
- Division of Chemistry and Chemical EngineeringCalifornia Institute of TechnologyPasadenaCaliforniaUSA
| | - Shyam M. Saladi
- Division of Chemistry and Chemical EngineeringCalifornia Institute of TechnologyPasadenaCaliforniaUSA
| | - William M. Clemons
- Division of Chemistry and Chemical EngineeringCalifornia Institute of TechnologyPasadenaCaliforniaUSA
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39
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Min H, Baek K, Lee A, Seok YJ, Choi Y. Genomic characterization of four Escherichia coli strains isolated from oral lichen planus biopsies. J Oral Microbiol 2021; 13:1905958. [PMID: 33828821 PMCID: PMC8009128 DOI: 10.1080/20002297.2021.1905958] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Oral lichen planus (OLP) is a chronic T cell-mediated inflammatory disease that affects the mucus membrane of the oral cavity. We previously proposed a potential role of intracellular bacteria detected within OLP lesions in the pathogenesis of OLP and isolated four Escherichia coli strains from OLP tissues that were phylogenetically close to K-12 MG1655 strain. We sequenced the genomes of the four OLP-isolated E. coli strains and generated 6.71 Gbp of Illumina MiSeq data (166–195x coverage per strain). The size of the assembled draft genomes was 4.69 Mbp, with a GC content of 50.7%, in which 4360 to 4367 protein-coding sequences per strain were annotated. We also identified 368 virulence factors and 53 antibiotic resistance genes. Comparative genomics revealed that the OLP-isolated strains shared more pangenome orthologous groups with pathogenic strains than did the K-12 MG1655 strain, a derivative of K-12 strain isolated from human feces. Although the OLP-isolated strains did not have the major virulence factors (VFs) of the pathogenic strains, a number of VFs involved in adherence/invasion, colonization, or systemic infection were identified. The genomic characteristics of E. coli first isolated from the oral cavity would benefit future investigations on the pathogenic potential of these bacteria.
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Affiliation(s)
- Huitae Min
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, Republic of Korea
| | - Keumjin Baek
- Department of Immunology and Molecular Microbiology, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, Republic of Korea
| | - Ahreum Lee
- Department of Immunology and Molecular Microbiology, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, Republic of Korea
| | - Yeong-Jae Seok
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, Republic of Korea
| | - Youngnim Choi
- Department of Immunology and Molecular Microbiology, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, Republic of Korea
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40
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Wong DK, Stark MS, Rader SD, Fast NM. Characterization of Pre-mRNA Splicing and Spliceosomal Machinery in Porphyridium purpureum and Evolutionary Implications for Red Algae. J Eukaryot Microbiol 2021; 68:e12844. [PMID: 33569840 DOI: 10.1111/jeu.12844] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 01/28/2021] [Accepted: 02/05/2021] [Indexed: 11/29/2022]
Abstract
Pre-mRNA splicing is a highly conserved eukaryotic process, but our understanding of it is limited by a historical focus on well-studied organisms such as humans and yeast. There is considerable diversity in mechanisms and components of pre-mRNA splicing, especially in lineages that have evolved under the pressures of genome reduction. The ancestor of red algae is thought to have undergone genome reduction prior to the lineage's radiation, resulting in overall gene and intron loss in extant groups. Previous studies on the extremophilic red alga Cyanidioschyzon merolae revealed an intron-sparse genome with a highly reduced spliceosome. To determine whether these features applied to other red algae, we investigated multiple aspects of pre-mRNA splicing in the mesophilic red alga Porphyridium purpureum. Through strand-specific RNA-Seq, we observed high levels of intron retention across a large number of its introns, and nearly half of the transcripts for these genes are not spliced at all. We also discovered a relationship between variability of 5' splice site sequences and levels of splicing. To further investigate the connections between intron retention and splicing machinery, we bioinformatically assembled the P. purpureum spliceosome, and biochemically verified the presence of snRNAs. While most other core spliceosomal components are present, our results suggest highly divergent or missing U1 snRNP proteins, despite the presence of an uncharacteristically long U1 snRNA. These unusual aspects highlight the diverse nature of pre-mRNA splicing that can be seen in lesser-studied eukaryotes, raising the importance of investigating fundamental eukaryotic processes outside of model organisms.
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Affiliation(s)
- Donald K Wong
- Department of Botany, University of British Columbia, 3156-6270 University Boulevard, Vancouver, BC, Canada
| | - Martha S Stark
- Department of Chemistry, University of Northern British Columbia, 3333 University Way, Prince George, BC, Canada
| | - Stephen D Rader
- Department of Chemistry, University of Northern British Columbia, 3333 University Way, Prince George, BC, Canada
| | - Naomi M Fast
- Department of Botany, University of British Columbia, 3156-6270 University Boulevard, Vancouver, BC, Canada
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41
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Hao Y, Lee HJ, Baraboo M, Burch K, Maurer T, Somarelli JA, Conant GC. Baby Genomics: Tracing the Evolutionary Changes That Gave Rise to Placentation. Genome Biol Evol 2021; 12:35-47. [PMID: 32053193 PMCID: PMC7144826 DOI: 10.1093/gbe/evaa026] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2020] [Indexed: 12/12/2022] Open
Abstract
It has long been challenging to uncover the molecular mechanisms behind striking morphological innovations such as mammalian pregnancy. We studied the power of a robust comparative orthology pipeline based on gene synteny to address such problems. We inferred orthology relations between human genes and genes from each of 43 other vertebrate genomes, resulting in ∼18,000 orthologous pairs for each genome comparison. By identifying genes that first appear coincident with origin of the placental mammals, we hypothesized that we would define a subset of the genome enriched for genes that played a role in placental evolution. We thus pinpointed orthologs that appeared before and after the divergence of eutherian mammals from marsupials. Reinforcing previous work, we found instead that much of the genetic toolkit of mammalian pregnancy evolved through the repurposing of preexisting genes to new roles. These genes acquired regulatory controls for their novel roles from a group of regulatory genes, many of which did in fact originate at the appearance of the eutherians. Thus, orthologs appearing at the origin of the eutherians are enriched in functions such as transcriptional regulation by Krüppel-associated box-zinc-finger proteins, innate immune responses, keratinization, and the melanoma-associated antigen protein class. Because the cellular mechanisms of invasive placentae are similar to those of metastatic cancers, we then used our orthology inferences to explore the association between placenta invasion and cancer metastasis. Again echoing previous work, we find that genes that are phylogenetically older are more likely to be implicated in cancer development.
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Affiliation(s)
- Yue Hao
- Bioinformatics Research Center, North Carolina State University
| | - Hyuk Jin Lee
- Division of Biological Sciences, University of Missouri-Columbia
| | | | | | | | - Jason A Somarelli
- Duke Cancer Institute, Duke University Medical Center.,Department of Medicine, Duke University School of Medicine
| | - Gavin C Conant
- Bioinformatics Research Center, North Carolina State University.,Division of Animal Sciences, University of Missouri-Columbia.,Program in Genetics, North Carolina State University.,Department of Biological Sciences, North Carolina State University
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42
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Rosselli R, La Porta N, Muresu R, Stevanato P, Concheri G, Squartini A. Pangenomics of the Symbiotic Rhizobiales. Core and Accessory Functions Across a Group Endowed with High Levels of Genomic Plasticity. Microorganisms 2021; 9:microorganisms9020407. [PMID: 33669391 PMCID: PMC7920277 DOI: 10.3390/microorganisms9020407] [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: 11/04/2020] [Revised: 02/10/2021] [Accepted: 02/11/2021] [Indexed: 11/16/2022] Open
Abstract
Pangenome analyses reveal major clues on evolutionary instances and critical genome core conservation. The order Rhizobiales encompasses several families with rather disparate ecological attitudes. Among them, Rhizobiaceae, Bradyrhizobiaceae, Phyllobacteriacreae and Xanthobacteriaceae, include members proficient in mutualistic symbioses with plants based on the bacterial conversion of N2 into ammonia (nitrogen-fixation). The pangenome of 12 nitrogen-fixing plant symbionts of the Rhizobiales was analyzed yielding total 37,364 loci, with a core genome constituting 700 genes. The percentage of core genes averaged 10.2% over single genomes, and between 5% to 7% were found to be plasmid-associated. The comparison between a representative reference genome and the core genome subset, showed the core genome highly enriched in genes for macromolecule metabolism, ribosomal constituents and overall translation machinery, while membrane/periplasm-associated genes, and transport domains resulted under-represented. The analysis of protein functions revealed that between 1.7% and 4.9% of core proteins could putatively have different functions.
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Affiliation(s)
- Riccardo Rosselli
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute of Sea Research, NL-1790 AB Den Burg, The Netherlands;
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, 03690 Alicante, Spain
| | - Nicola La Porta
- Department of Sustainable Agrobiosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, 38098 San Michele all’Adige, Italy;
- MOUNTFOR Project Centre, European Forest Institute, 38098 San Michele all’Adige, Italy
| | - Rosella Muresu
- Institute of Animal Production Systems in Mediterranean Environments-National Research Council, 07040 Sassari, Italy;
| | - Piergiorgio Stevanato
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Legnaro, Italy; (P.S.); (G.C.)
| | - Giuseppe Concheri
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Legnaro, Italy; (P.S.); (G.C.)
| | - Andrea Squartini
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Legnaro, Italy; (P.S.); (G.C.)
- Correspondence: ; Tel.: +39-049-8272-923
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Sastry AV, Hu A, Heckmann D, Poudel S, Kavvas E, Palsson BO. Independent component analysis recovers consistent regulatory signals from disparate datasets. PLoS Comput Biol 2021; 17:e1008647. [PMID: 33529205 PMCID: PMC7888660 DOI: 10.1371/journal.pcbi.1008647] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 02/17/2021] [Accepted: 12/18/2020] [Indexed: 01/03/2023] Open
Abstract
The availability of bacterial transcriptomes has dramatically increased in recent years. This data deluge could result in detailed inference of underlying regulatory networks, but the diversity of experimental platforms and protocols introduces critical biases that could hinder scalable analysis of existing data. Here, we show that the underlying structure of the E. coli transcriptome, as determined by Independent Component Analysis (ICA), is conserved across multiple independent datasets, including both RNA-seq and microarray datasets. We subsequently combined five transcriptomics datasets into a large compendium containing over 800 expression profiles and discovered that its underlying ICA-based structure was still comparable to that of the individual datasets. With this understanding, we expanded our analysis to over 3,000 E. coli expression profiles and predicted three high-impact regulons that respond to oxidative stress, anaerobiosis, and antibiotic treatment. ICA thus enables deep analysis of disparate data to uncover new insights that were not visible in the individual datasets. Cells adapt to diverse environments by regulating gene expression. Genome-wide measurements of gene expression levels have exponentially increased in recent years, but successful integration and analysis of these datasets are limited. Recently, we showed that independent component analysis (ICA), a signal deconvolution algorithm, can separate a large bacterial gene expression dataset into groups of co-regulated genes. This previous study focused on data generated by a standardized pipeline and did not address whether ICA extracts the same quantitative co-expression signals across expression profiling platforms. In this study, we show that ICA finds similar co-regulation patterns underlying multiple gene expression datasets and can be used as a tool to integrate and interpret diverse datasets. Using a dataset containing over 3,000 expression profiles, we predicted three new regulons and characterized their activities. Since large, standardized expression datasets only exist for a few bacterial strains, these results broaden the possible applications of this tool to better understand transcriptional regulation across a wide range of microbes.
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Affiliation(s)
- Anand V. Sastry
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
| | - Alyssa Hu
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
| | - David Heckmann
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
| | - Saugat Poudel
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
| | - Erol Kavvas
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
- * E-mail:
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44
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De Vega D, Holden N, Hedley PE, Morris J, Luna E, Newton A. Chitosan primes plant defence mechanisms against Botrytis cinerea, including expression of Avr9/Cf-9 rapidly elicited genes. PLANT, CELL & ENVIRONMENT 2021; 44:290-303. [PMID: 33094513 PMCID: PMC7821246 DOI: 10.1111/pce.13921] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/21/2020] [Accepted: 06/29/2020] [Indexed: 05/10/2023]
Abstract
Current crop protection strategies against the fungal pathogen Botrytis cinerea rely on a combination of conventional fungicides and host genetic resistance. However, due to pathogen evolution and legislation in the use of fungicides, these strategies are not sufficient to protect plants against this pathogen. Defence elicitors can stimulate plant defence mechanisms through a phenomenon known as defence priming. Priming results in a faster and/or stronger expression of resistance upon pathogen recognition by the host. This work aims to study defence priming by a commercial formulation of the elicitor chitosan. Treatments with chitosan result in induced resistance (IR) in solanaceous and brassicaceous plants. In tomato plants, enhanced resistance has been linked with priming of callose deposition and accumulation of the plant hormone jasmonic acid (JA). Large-scale transcriptomic analysis revealed that chitosan primes gene expression at early time-points after infection. In addition, two novel tomato genes with a characteristic priming profile were identified, Avr9/Cf-9 rapidly elicited protein 75 (ACRE75) and 180 (ACRE180). Transient and stable over-expression of ACRE75, ACRE180 and their Nicotiana benthamiana homologs, revealed that they are positive regulators of plant resistance against B. cinerea. This provides valuable information in the search for strategies to protect Solanaceae plants against B. cinerea.
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Affiliation(s)
| | - Nicola Holden
- The James Hutton InstituteDundeeUK
- Scotland's Rural College, Aberdeen CampusAberdeenUK
| | | | | | - Estrella Luna
- School of BiosciencesUniversity of BirminghamBirminghamUK
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Arraes FBM, Martins-de-Sa D, Noriega Vasquez DD, Melo BP, Faheem M, de Macedo LLP, Morgante CV, Barbosa JARG, Togawa RC, Moreira VJV, Danchin EGJ, Grossi-de-Sa MF. Dissecting protein domain variability in the core RNA interference machinery of five insect orders. RNA Biol 2020; 18:1653-1681. [PMID: 33302789 DOI: 10.1080/15476286.2020.1861816] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
RNA interference (RNAi)-mediated gene silencing can be used to control specific insect pest populations. Unfortunately, the variable efficiency in the knockdown levels of target genes has narrowed the applicability of this technology to a few species. Here, we examine the current state of knowledge regarding the miRNA (micro RNA) and siRNA (small interfering RNA) pathways in insects and investigate the structural variability at key protein domains of the RNAi machinery. Our goal was to correlate domain variability with mechanisms affecting the gene silencing efficiency. To this end, the protein domains of 168 insect species, encompassing the orders Coleoptera, Diptera, Hemiptera, Hymenoptera, and Lepidoptera, were analysed using our pipeline, which takes advantage of meticulous structure-based sequence alignments. We used phylogenetic inference and the evolutionary rate coefficient (K) to outline the variability across domain regions and surfaces. Our results show that four domains, namely dsrm, Helicase, PAZ and Ribonuclease III, are the main contributors of protein variability in the RNAi machinery across different insect orders. We discuss the potential roles of these domains in regulating RNAi-mediated gene silencing and the role of loop regions in fine-tuning RNAi efficiency. Additionally, we identified several order-specific singularities which indicate that lepidopterans have evolved differently from other insect orders, possibly due to constant coevolution with plants and viruses. In conclusion, our results highlight several variability hotspots that deserve further investigation in order to improve the application of RNAi technology in the control of insect pests.
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Affiliation(s)
| | - Diogo Martins-de-Sa
- Departamento De Biologia Celular, Universidade De Brasília, Brasília-DF, Brazil
| | - Daniel D Noriega Vasquez
- Plant-Pest Molecular Interaction Laboratory (LIMPP), Brasilia, Brasília-DF, Brazil.,Catholic University of Brasília, Brasília-DF, Brazil
| | - Bruno Paes Melo
- Plant-Pest Molecular Interaction Laboratory (LIMPP), Brasilia, Brasília-DF, Brazil.,Viçosa University, UFV, Viçosa-MG, Brazil
| | - Muhammad Faheem
- Plant-Pest Molecular Interaction Laboratory (LIMPP), Brasilia, Brasília-DF, Brazil.,Department of Biological Sciences, National University of Medical Sciences, Punjab, Pakistan
| | | | - Carolina Vianna Morgante
- Plant-Pest Molecular Interaction Laboratory (LIMPP), Brasilia, Brasília-DF, Brazil.,Embrapa Semiarid, Petrolina-PE, Brazil.,National Institute of Science and Technology, Jakarta Embrapa-Brazil
| | | | - Roberto Coiti Togawa
- Plant-Pest Molecular Interaction Laboratory (LIMPP), Brasilia, Brasília-DF, Brazil
| | - Valdeir Junio Vaz Moreira
- Biotechnology Center, Brazil.,Plant-Pest Molecular Interaction Laboratory (LIMPP), Brasilia, Brasília-DF, Brazil.,Departamento De Biologia Celular, Universidade De Brasília, Brasília-DF, Brazil
| | - Etienne G J Danchin
- National Institute of Science and Technology, Jakarta Embrapa-Brazil.,INRAE, Université Côte d'Azur, CNRS, Institut Sophia Agrobiotech, Sophia-Antipolis, France
| | - Maria Fatima Grossi-de-Sa
- Plant-Pest Molecular Interaction Laboratory (LIMPP), Brasilia, Brasília-DF, Brazil.,Catholic University of Brasília, Brasília-DF, Brazil.,National Institute of Science and Technology, Jakarta Embrapa-Brazil
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Harrison MC, Chernyshova AM, Thompson GJ. No obvious transcriptome-wide signature of indirect selection in termites. J Evol Biol 2020; 34:403-415. [PMID: 33290587 DOI: 10.1111/jeb.13749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 11/16/2020] [Accepted: 11/30/2020] [Indexed: 11/26/2022]
Abstract
The evolution of sterile helper castes in social insects implies selection on genes that underlie variation in this nonreproductive phenotype. These focal genes confer no direct fitness and are presumed to evolve through indirect fitness effects on the helper's reproducing relatives. This separation of a gene's phenotypic effect on one caste and its fitness effect on another suggests that genes for this and other forms of reproductive altruism are buffered from selection and will thus evolve closer to the neutral rate than genes directly selected for selfish reproduction. We test this hypothesis by comparing the strength of selection at loci associated in their expression with reproductive versus sterile castes in termites. Specifically, we gather caste-biased gene expression data from four termite transcriptomes and measure the global dN/dS ratio across gene sets and phylogenetic lineages. We find that the majority of examined orthologous gene groups show patterns of nucleotide substitution that are consistent with strong purifying selection and display little evidence for distinct signatures of direct versus indirect selection in reproductive and sterile castes. For one particular species (Reticulitermes flavipes), the strength of purifying selection is relaxed in a reproductive nymph-biased gene set, which opposes the nearly neutral idea. In other species, the synonymous rate (dS) alone was often found to be the highest in the sterile worker caste, suggesting a more subtle signature of indirect selection or an altogether different relationship between caste-biased expression and rates of molecular evolution.
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Affiliation(s)
- Mark C Harrison
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
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Genome-Wide Analysis of Nubian Ibex Reveals Candidate Positively Selected Genes That Contribute to Its Adaptation to the Desert Environment. Animals (Basel) 2020; 10:ani10112181. [PMID: 33266380 PMCID: PMC7700370 DOI: 10.3390/ani10112181] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/31/2020] [Accepted: 11/03/2020] [Indexed: 12/21/2022] Open
Abstract
Simple Summary The Nubian ibex is a wild relative of the domestic goat found in hot deserts of Northern Africa and Arabia. The domestic goat is an important livestock species that is mainly found in arid and semi-arid regions of Africa and Asia. The Nubian ibex is well adapted to challenging environments in hot deserts characterized by high diurnal temperatures, intense solar radiation, and scarce water resources. It is therefore important to understand the genetic basis of its adaptation for scientific and economic importance. To identify genes with adaptive traits, the Nubian ibex genome was sequenced and compared with that of related mammals. We identified twenty-five genes under selection in the Nubian ibex that play diverse biological roles such as immune response, visual development, signal transduction, and reproduction. Three other genes under adaptive evolution involved in protective functions of the skin against damaging solar radiation in the desert were identified in Nubian ibex genome. Our finding provides valuable genomic insights into the adaptation of Nubian ibex to desert environments. The genomic information generated in this study can be used in developing appropriate breeding programs aimed at enhancing adaptation of local goats to less favorable habitats in response to changing climates. Abstract The domestic goat (Capra hircus) is an important livestock species with a geographic range spanning all continents, including arid and semi-arid regions of Africa and Asia. The Nubian ibex (Capra nubiana), a wild relative of the domestic goat inhabiting the hot deserts of Northern Africa and the Arabian Peninsula, is well-adapted to challenging environments in hot deserts characterized by intense solar radiation, thermal extremes, and scarce water resources. The economic importance of C. hircus breeds, as well as the current trends of global warming, highlights the need to understand the genetic basis of adaptation of C. nubiana to the desert environments. In this study, the genome of a C. nubiana individual was sequenced at an average of 37x coverage. Positively selected genes were identified by comparing protein-coding DNA sequences of C. nubiana and related species using dN/dS statistics. A total of twenty-two positively selected genes involved in diverse biological functions such as immune response, protein ubiquitination, olfactory transduction, and visual development were identified. In total, three of the twenty-two positively selected genes are involved in skin barrier development and function (ATP binding cassette subfamily A member 12, Achaete-scute family bHLH transcription factor 4, and UV stimulated scaffold protein A), suggesting that C. nubiana has evolved skin protection strategies against the damaging solar radiations that prevail in deserts. The positive selection signatures identified here provide new insights into the potential adaptive mechanisms to hot deserts in C. nubiana.
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48
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Hernández-Salmerón JE, Moreno-Hagelsieb G. Progress in quickly finding orthologs as reciprocal best hits: comparing blast, last, diamond and MMseqs2. BMC Genomics 2020; 21:741. [PMID: 33099302 PMCID: PMC7585182 DOI: 10.1186/s12864-020-07132-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 10/09/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Finding orthologs remains an important bottleneck in comparative genomics analyses. While the authors of software for the quick comparison of protein sequences evaluate the speed of their software and compare their results against the most usual software for the task, it is not common for them to evaluate their software for more particular uses, such as finding orthologs as reciprocal best hits (RBH). Here we compared RBH results obtained using software that runs faster than blastp. Namely, lastal, diamond, and MMseqs2. RESULTS We found that lastal required the least time to produce results. However, it yielded fewer results than any other program when comparing the proteins encoded by evolutionarily distant genomes. The program producing the most similar number of RBH to blastp was diamond ran with the "ultra-sensitive" option. However, this option was diamond's slowest, with the "very-sensitive" option offering the best balance between speed and RBH results. The speeding up of the programs was much more evident when dealing with eukaryotic genomes, which code for more numerous proteins. For example, lastal took a median of approx. 1.5% of the blastp time to run with bacterial proteomes and 0.6% with eukaryotic ones, while diamond with the very-sensitive option took 7.4% and 5.2%, respectively. Though estimated error rates were very similar among the RBH obtained with all programs, RBH obtained with MMseqs2 had the lowest error rates among the programs tested. CONCLUSIONS The fast algorithms for pairwise protein comparison produced results very similar to blast in a fraction of the time, with diamond offering the best compromise in speed, sensitivity and quality, as long as a sensitivity option, other than the default, was chosen.
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Affiliation(s)
| | - Gabriel Moreno-Hagelsieb
- Wilfrid Laurier University, Department of Biology, 75 University Ave W, Waterloo, N2L 3C5 ON Canada
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49
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Nakai R, Naganuma T, Tazato N, Morohoshi S, Koide T. Cell Plasticity and Genomic Structure of a Novel Filterable Rhizobiales Bacterium that Belongs to a Widely Distributed Lineage. Microorganisms 2020; 8:microorganisms8091373. [PMID: 32906802 PMCID: PMC7564735 DOI: 10.3390/microorganisms8091373] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 08/29/2020] [Accepted: 09/04/2020] [Indexed: 01/28/2023] Open
Abstract
Rhizobiales bacterium strain IZ6 is a novel filterable bacterium that was isolated from a suspension filtrate (<0.22 µm) of soil collected in Shimane Prefecture, western Japan. Additional closely related isolates were recovered from filterable fractions of terrestrial environmental samples collected from other places in Japan; the Gobi Desert, north-central China; and Svalbard, Arctic Norway. These findings indicate a wide distribution of this lineage. This study reports the cell variation and genomic structure of IZ6. When cultured at lower temperatures (4 °C and 15 °C), this strain contained ultra-small cells and cell-like particles in the filtrate. PacBio sequencing revealed that this chromosome (3,114,641 bp) contained 3150 protein-coding, 51 tRNA, and three rRNA genes. IZ6 showed low 16S rRNA gene sequence identity (<97%) and low average nucleotide identity (<76%) with its closest known relative, Flaviflagellibacter deserti. Unlike the methylotrophic bacteria and nitrogen-fixing bacteria in related genera, there were no genes that encoded enzymes for one-carbon-compound utilization and nitrogen fixation in the IZ6 genome; the genes related to nitrate and nitrite reductase are retained and those related to the cell membrane function tend to be slightly enriched in the genome. This genomic information helps elucidate the eco-physiological function of a phenotypically heterogeneous and diverse Rhizobiales group.
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Affiliation(s)
- Ryosuke Nakai
- Microbial Ecology and Technology Research Group, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-higashi, Toyohira-ku, Sapporo 062-8517, Japan
- Correspondence:
| | - Takeshi Naganuma
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashihiroshima 739-8528, Japan;
| | - Nozomi Tazato
- Technical Department, TechnoSuruga Laboratory Co. Ltd., 330 Nagasaki, Shimizu-ku, Shizuoka 424-0065, Japan; (N.T.); (S.M.); (T.K.)
| | - Sho Morohoshi
- Technical Department, TechnoSuruga Laboratory Co. Ltd., 330 Nagasaki, Shimizu-ku, Shizuoka 424-0065, Japan; (N.T.); (S.M.); (T.K.)
| | - Tomomi Koide
- Technical Department, TechnoSuruga Laboratory Co. Ltd., 330 Nagasaki, Shimizu-ku, Shizuoka 424-0065, Japan; (N.T.); (S.M.); (T.K.)
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50
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Heger P, Zheng W, Rottmann A, Panfilio KA, Wiehe T. The genetic factors of bilaterian evolution. eLife 2020; 9:e45530. [PMID: 32672535 PMCID: PMC7535936 DOI: 10.7554/elife.45530] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 07/03/2020] [Indexed: 12/13/2022] Open
Abstract
The Cambrian explosion was a unique animal radiation ~540 million years ago that produced the full range of body plans across bilaterians. The genetic mechanisms underlying these events are unknown, leaving a fundamental question in evolutionary biology unanswered. Using large-scale comparative genomics and advanced orthology evaluation techniques, we identified 157 bilaterian-specific genes. They include the entire Nodal pathway, a key regulator of mesoderm development and left-right axis specification; components for nervous system development, including a suite of G-protein-coupled receptors that control physiology and behaviour, the Robo-Slit midline repulsion system, and the neurotrophin signalling system; a high number of zinc finger transcription factors; and novel factors that previously escaped attention. Contradicting the current view, our study reveals that genes with bilaterian origin are robustly associated with key features in extant bilaterians, suggesting a causal relationship.
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Affiliation(s)
- Peter Heger
- Institute for Genetics, Cologne Biocenter, University of CologneCologneGermany
| | - Wen Zheng
- Institute for Genetics, Cologne Biocenter, University of CologneCologneGermany
| | - Anna Rottmann
- Institute for Genetics, Cologne Biocenter, University of CologneCologneGermany
| | - Kristen A Panfilio
- Institute for Zoology: Developmental Biology, Cologne Biocenter, University of CologneCologneGermany
- School of Life Sciences, University of Warwick, Gibbet Hill CampusCoventryUnited Kingdom
| | - Thomas Wiehe
- Institute for Genetics, Cologne Biocenter, University of CologneCologneGermany
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