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Martins JR, Pinheiro DG, Ahmed ACC, Giuliatti S, Mizzen CA, Bitondi MMG. Genome-wide analysis of the chromatin sites targeted by HEX 70a storage protein in the honeybee brain and fat body. Insect Mol Biol 2023; 32:277-304. [PMID: 36630080 DOI: 10.1111/imb.12830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 12/12/2022] [Indexed: 05/15/2023]
Abstract
Hexamerins, the proteins massively stored in the larval haemolymph of insects, are gradually used throughout metamorphosis as a source of raw material and energy for the development of adult tissues. Such behaviour defined hexamerins as storage proteins. Immunofluorescence experiments coupled with confocal microscopy show a hexamerin, HEX 70a, in the nucleus of the brain and fat body cells from honeybee workers, an unexpected localization for a storage protein. HEX 70a colocalizes with fibrillarin, a nucleolar-specific protein and H3 histone, thus suggesting a potential role as a chromatin-binding protein. This was investigated through chromatin immunoprecipitation and high-throughput DNA sequencing (ChIP-seq). The significant HEX 70a-DNA binding sites were mainly localized at the intergenic, promoter and intronic regions. HEX 70a targeted DNA stretches mapped to the genomic regions encompassing genes with relevant functional attributes. Several HEX 70a targeted genes were associated with H3K27ac or/and H3K27me3, known as active and repressive histone marks. Brain and fat body tissues shared a fraction of the HEX 70 targeted genes, and tissue-specific targets were also detected. The presence of overrepresented DNA motifs in the binding sites is consistent with specific HEX 70a-chromatin association. In addition, a search for HEX 70a targets in RNA-seq public libraries of fat bodies from nurses and foragers revealed differentially expressed targets displaying hex 70a-correlated developmental expression, thus supporting a regulatory activity for HEX 70a. Our results support the premise that HEX 70a is a moonlighting protein that binds chromatin and has roles in the brain and fat body cell nuclei, apart from its canonical role as a storage protein.
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Affiliation(s)
- Juliana R Martins
- Faculdade de Medicina de Ribeirão Preto, Departamento de Genética, Ribeirão Preto, Brazil
| | - Daniel G Pinheiro
- Departamento de Biotecnologia Agropecuária e Ambiental, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal, Brazil
| | - Amy C C Ahmed
- University of Illinois at Urbana-Champaign, Carl R. Woese Institute for Genomic Biology, Urbana, Illinois, USA
| | - Silvana Giuliatti
- Faculdade de Medicina de Ribeirão Preto, Departamento de Genética, Ribeirão Preto, Brazil
| | - Craig A Mizzen
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Márcia M G Bitondi
- Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Departamento de Biologia, Ribeirão Preto, Brazil
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2
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Silva SR, Miranda VFO, Michael TP, Płachno BJ, Matos RG, Adamec L, Pond SLK, Lucaci AG, Pinheiro DG, Varani AM. The phylogenomics and evolutionary dynamics of the organellar genomes in carnivorous Utricularia and Genlisea species (Lentibulariaceae). Mol Phylogenet Evol 2023; 181:107711. [PMID: 36693533 DOI: 10.1016/j.ympev.2023.107711] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/13/2023] [Accepted: 01/18/2023] [Indexed: 01/22/2023]
Abstract
Utricularia and Genlisea are highly specialized carnivorous plants whose phylogenetic history has been poorly explored using phylogenomic methods. Additional sampling and genomic data are needed to advance our phylogenetic and taxonomic knowledge of this group of plants. Within a comparative framework, we present a characterization of plastome (PT) and mitochondrial (MT) genes of 26 Utricularia and six Genlisea species, with representatives of all subgenera and growth habits. All PT genomes maintain similar gene content, showing minor variation across the genes located between the PT junctions. One exception is a major variation related to different patterns in the presence and absence of ndh genes in the small single copy region, which appears to follow the phylogenetic history of the species rather than their lifestyle. All MT genomes exhibit similar gene content, with most differences related to a lineage-specific pseudogenes. We find evidence for episodic positive diversifying selection in PT and for most of the Utricularia MT genes that may be related to the current hypothesis that bladderworts' nuclear DNA is under constant ROS oxidative DNA damage and unusual DNA repair mechanisms, or even low fidelity polymerase that bypass lesions which could also be affecting the organellar genomes. Finally, both PT and MT phylogenetic trees were well resolved and highly supported, providing a congruent phylogenomic hypothesis for Utricularia and Genlisea clade given the study sampling.
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Affiliation(s)
- Saura R Silva
- UNESP - São Paulo State University, School of Agricultural and Veterinarian Sciences, Department of Agricultural and Environmental Biotechnology, Campus Jaboticabal, CEP 14884-900 SP, Brazil.
| | - Vitor F O Miranda
- UNESP - São Paulo State University, School of Agricultural and Veterinarian Sciences, Department of Biology, Laboratory of Plant Systematics, Campus Jaboticabal, CEP 14884-900 SP, Brazil.
| | - Todd P Michael
- Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
| | - Bartosz J Płachno
- Department of Plant Cytology and Embryology, Institute of Botany, Faculty of Biology, Jagiellonian University in Kraków, Gronostajowa 9 St., 30-387 Cracow, Poland.
| | - Ramon G Matos
- UNESP - São Paulo State University, School of Agricultural and Veterinarian Sciences, Department of Biology, Laboratory of Plant Systematics, Campus Jaboticabal, CEP 14884-900 SP, Brazil.
| | - Lubomir Adamec
- Department of Experimental and Functional Morphology, Institute of Botany CAS, Dukelská 135, CZ-379 01 Třeboň, Czech Republic.
| | - Sergei L K Pond
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA 19122, USA.
| | - Alexander G Lucaci
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA 19122, USA.
| | - Daniel G Pinheiro
- UNESP - São Paulo State University, School of Agricultural and Veterinarian Sciences, Department of Agricultural and Environmental Biotechnology, Campus Jaboticabal, CEP 14884-900 SP, Brazil.
| | - Alessandro M Varani
- UNESP - São Paulo State University, School of Agricultural and Veterinarian Sciences, Department of Agricultural and Environmental Biotechnology, Campus Jaboticabal, CEP 14884-900 SP, Brazil.
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3
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Martelli F, Falcon T, Pinheiro DG, Simões ZLP, Nunes FMF. Worker bees (Apis mellifera) deprived of pollen in the first week of adulthood exhibit signs of premature aging. Insect Biochem Mol Biol 2022; 146:103774. [PMID: 35470035 DOI: 10.1016/j.ibmb.2022.103774] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 04/18/2022] [Accepted: 04/18/2022] [Indexed: 06/14/2023]
Abstract
Pollinator populations, including bees, are in rapid decline in many parts of the world, raising concerns over the future of ecosystems and food production. Among the factors involved in these declines, poor nutrition deserves attention. The diet consumed by adult worker honeybees (Apis mellifera) is crucial for their behavioral maturation, i.e., the progressive division of labor they perform, such as nurse bees initially and later in life as foragers. Poor pollen nutrition is known to reduce the workers' lifespan, but the underlying physiological and genetic mechanisms are not fully understood. Here we investigate how the lack of pollen in the diet of workers during their first week of adult life can affect age-related phenotypes. During the first seven days of adult life, newly emerged workers were fed either a pollen-deprived (PD) diet mimicking that of an older bee, or a control pollen-rich (PR) diet, as typically consumed by young bees. The PD-fed bees showed alterations in their fat body transcriptome, such as a switch from a protein-lipid based metabolism to a carbohydrate-based metabolism, and a reduced expression of genes involved with immune response. The absence of pollen in the diet also led to an accumulation of oxidative stress markers in fat body tissue and alterations in the cuticular hydrocarbon profiles, which became similar to those of chronologically older bees. Together, our data indicate that the absence of pollen during first week of adulthood triggers the premature onset of an aging-related worker phenotype.
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Affiliation(s)
- Felipe Martelli
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, 14049-900, Ribeirão Preto, SP, Brazil
| | - Tiago Falcon
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, 14049-900, Ribeirão Preto, SP, Brazil
| | - Daniel G Pinheiro
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, 14049-900, Ribeirão Preto, SP, Brazil
| | - Zilá L P Simões
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, 14049-900, Ribeirão Preto, SP, Brazil; Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, 14049-900, Ribeirão Preto, SP, Brazil
| | - Francis M F Nunes
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, 14049-900, Ribeirão Preto, SP, Brazil; Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, Rod. Washington Luís - km 235, 13565-905, São Carlos, SP, Brazil.
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4
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Machado NAF, Martin JE, Barbosa-Filho JAD, Dias CTS, Pinheiro DG, de Oliveira KPL, Souza-Junior JBF. Identification of trailer heat zones and associated heat stress in weaner pigs transported by road in tropical climates. J Therm Biol 2021; 97:102882. [PMID: 33863446 DOI: 10.1016/j.jtherbio.2021.102882] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 08/10/2020] [Accepted: 02/14/2021] [Indexed: 11/26/2022]
Abstract
Heat stress is major welfare concern during transport of pigs in tropical climates, which can also lead to direct production costs. This study evaluated the dynamics of heat zones through the load and their relationship with heat stress of weaner pigs during road transport in a tropical climate. Both environmental (e.g. temperature and relative humidity) and physiological (e.g. respiratory frequency and lactate) measures were recorded from four vehicle journeys (70 km distance, 216 weaner pigs within each trailer load) within Ceará, northeastern Brazil. Geostatistics and fluid dynamics simulation techniques were applied to understand the dynamics of heat zones and ventilation patterns the truckload. Statistics based on canonical discriminant analysis and ANOVA were performed to verify the relationship between heat zones and heat stress in pigs. The results showed that, during transport, the generation of heat zones occurred with different magnitudes along the load (P < 0.05), which was harmonized by the ventilation dynamics. There was a heat core with high energy content, in the front region of the lower deck (LD) of the trailer. In this zone, weaners pigs had higher rectal temperature (+1.8 °C temperature difference), respiratory frequency (LD = 94 ± 1.3 breaths/min; UD = 86 ± 1.3 breaths/min), and blood cortisol concentration (LD = 32.9 ± 0.8 ng/mL; UD = 30.18 ± 0.6 ng/mL) (all P < 0.05). Weaners pigs transported in the upper deck (UD) compartments had the highest skin temperature (LD = 38.13 ± 0.3 °C; UD = 38.9 ± 0.22 °C) and the highest mean values of blood lactate (LD = 65.5 ± 1.11 m/M; UD = 71.60 ± 1.19 m/M) and Creatine kinase (LD = 3891.23 ± 69U/L; UD = 4107.43 ± 62U/L) (P < 0.05). Weaners transported in compartments of the LD of trailer were more susceptible to heat stress, while weaners in the UD compartments were more susceptible to physical stress and muscle exhaustion. These results provide additional evidence of heat zones within trailer compartments and highlight the requirement for the planning of pig transport operations in tropical climates to mitigate risks of heat stress.
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Affiliation(s)
- Nítalo A F Machado
- Department of Agricultural Engineering, Universidade Federal do Ceará, Fortaleza, Brazil.
| | - Jessica E Martin
- The Royal (Dick) School of Veterinary Studies and the Roslin Institute, The College of Medicine and Veterinary Medicine, Easter Bush Campus, The University of Edinburgh, Edinburgh, EH25 9RG, UK
| | | | - Carlos T S Dias
- Department of Exact Sciences, Universidade de São Paulo, Piracicaba, Brazil
| | - Daniel G Pinheiro
- Department of Agricultural Engineering, Universidade Federal do Ceará, Fortaleza, Brazil
| | - Kenio P L de Oliveira
- Department of Agricultural Engineering, Universidade Federal do Ceará, Fortaleza, Brazil
| | - João B F Souza-Junior
- Laboratory of Biometeorology and Environmental Biophysics, Universidade Federal Rural do Semi-Árido, Mossoró, Brazil
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5
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de Paula Junior DE, de Oliveira MT, Bruscadin JJ, Pinheiro DG, Bomtorin AD, Coelho Júnior VG, Moda LMR, Simões ZLP, Barchuk AR. Caste-specific gene expression underlying the differential adult brain development in the honeybee Apis mellifera. Insect Mol Biol 2021; 30:42-56. [PMID: 33044766 DOI: 10.1111/imb.12671] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 09/08/2020] [Accepted: 10/07/2020] [Indexed: 06/11/2023]
Abstract
Apis mellifera adult workers feature more developed key brain regions than queens, which allows them to cope with the broad range of duties they need to perform in a colony. However, at the end of larval development, the brain of queens is largely more developed than that of workers. Major morphogenetic changes take place after metamorphosis that shift caste-specific brain development. Here, we tested the hypothesis that this phenomenon is hormonally governed and involves differential gene expression. Our molecular screening approach revealed a set of differentially expressed genes in Pp (first pharate-adult phase) brains between castes mainly coding for tissue remodelling and energy-converting proteins (e.g. hex 70a and ATPsynβ). An in-depth qPCR analysis of the transcriptional behaviour during pupal and pharate-adult developmental stage in both castes and in response to artificially augmented hormone titres of 18 genes/variants revealed that: i. subtle differences in hormone titres between castes might be responsible for the differential expression of the EcR and insulin/insulin-like signalling (IIS) pathway genes; ii. the morphogenetic activity of the IIS in brain development must be mediated by ILP-2, iii. which together with the tum, mnb and caspase system, can constitute the molecular effectors of the caste-specific opposing brain developmental trajectories.
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Affiliation(s)
- D E de Paula Junior
- Departamento de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, UNIFAL-MG, Alfenas, Brazil
| | - M T de Oliveira
- Departamento de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, UNIFAL-MG, Alfenas, Brazil
| | - J J Bruscadin
- Departamento de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, UNIFAL-MG, Alfenas, Brazil
| | - D G Pinheiro
- Faculdade de Ciências Agrárias e Veterinárias, UNESP - Universidade Estadual Paulista, São Paulo, Brazil
| | - A D Bomtorin
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - V G Coelho Júnior
- Departamento de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, UNIFAL-MG, Alfenas, Brazil
| | - L M R Moda
- Departamento de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, UNIFAL-MG, Alfenas, Brazil
| | - Z L P Simões
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - A R Barchuk
- Departamento de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, UNIFAL-MG, Alfenas, Brazil
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6
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Silva DBS, Fonseca LFS, Pinheiro DG, Magalhães AFB, Muniz MMM, Ferro JA, Baldi F, Chardulo LAL, Schnabel RD, Taylor JF, Albuquerque LG. Spliced genes in muscle from Nelore Cattle and their association with carcass and meat quality. Sci Rep 2020; 10:14701. [PMID: 32895448 PMCID: PMC7477197 DOI: 10.1038/s41598-020-71783-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 08/04/2020] [Indexed: 01/31/2023] Open
Abstract
Transcript data obtained by RNA-Seq were used to identify differentially expressed alternatively spliced genes in ribeye muscle tissue between Nelore cattle that differed in their ribeye area (REA) or intramuscular fat content (IF). A total of 166 alternatively spliced transcripts from 125 genes were significantly differentially expressed in ribeye muscle between the highest and lowest REA groups (p ≤ 0.05). For animals selected on their IF content, 269 alternatively spliced transcripts from 219 genes were differentially expressed in ribeye muscle between the highest and lowest IF animals. Cassette exons and alternative 3′ splice sites were the most frequently found alternatively spliced transcripts for REA and IF content. For both traits, some differentially expressed alternatively spliced transcripts belonged to myosin and myotilin gene families. The hub transcripts were identified for REA (LRRFIP1, RCAN1 and RHOBTB1) and IF (TRIP12, HSPE1 and MAP2K6) have an important role to play in muscle cell degradation, development and motility. In general, transcripts were found for both traits with biological process GO terms that were involved in pathways related to protein ubiquitination, muscle differentiation, lipids and hormonal systems. Our results reinforce the biological importance of these known processes but also reveal new insights into the complexity of the whole cell muscle mRNA of Nelore cattle.
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Affiliation(s)
- Danielly B S Silva
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, Brazil.
| | - Larissa F S Fonseca
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, Brazil
| | - Daniel G Pinheiro
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, Brazil
| | - Ana F B Magalhães
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, Brazil
| | - Maria M M Muniz
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, Brazil
| | - Jesus A Ferro
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, Brazil.,National Council for Scientific and Technological Development (CNPq), Brasilia, DF, Brazil
| | - Fernando Baldi
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, Brazil.,National Council for Scientific and Technological Development (CNPq), Brasilia, DF, Brazil
| | - Luis A L Chardulo
- School of Veterinary and Animal Science, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Robert D Schnabel
- Division of Animal Sciences, University of Missouri Columbia, Columbia, MO, USA
| | - Jeremy F Taylor
- Division of Animal Sciences, University of Missouri Columbia, Columbia, MO, USA
| | - Lucia G Albuquerque
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, Brazil. .,National Council for Scientific and Technological Development (CNPq), Brasilia, DF, Brazil.
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7
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de Paula Freitas FC, Lourenço AP, Nunes FMF, Paschoal AR, Abreu FCP, Barbin FO, Bataglia L, Cardoso-Júnior CAM, Cervoni MS, Silva SR, Dalarmi F, Del Lama MA, Depintor TS, Ferreira KM, Gória PS, Jaskot MC, Lago DC, Luna-Lucena D, Moda LM, Nascimento L, Pedrino M, Oliveira FR, Sanches FC, Santos DE, Santos CG, Vieira J, Barchuk AR, Hartfelder K, Simões ZLP, Bitondi MMG, Pinheiro DG. The nuclear and mitochondrial genomes of Frieseomelitta varia - a highly eusocial stingless bee (Meliponini) with a permanently sterile worker caste. BMC Genomics 2020; 21:386. [PMID: 32493270 PMCID: PMC7268684 DOI: 10.1186/s12864-020-06784-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 05/14/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Most of our understanding on the social behavior and genomics of bees and other social insects is centered on the Western honey bee, Apis mellifera. The genus Apis, however, is a highly derived branch comprising less than a dozen species, four of which genomically characterized. In contrast, for the equally highly eusocial, yet taxonomically and biologically more diverse Meliponini, a full genome sequence was so far available for a single Melipona species only. We present here the genome sequence of Frieseomelitta varia, a stingless bee that has, as a peculiarity, a completely sterile worker caste. RESULTS The assembly of 243,974,526 high quality Illumina reads resulted in a predicted assembled genome size of 275 Mb composed of 2173 scaffolds. A BUSCO analysis for the 10,526 predicted genes showed that these represent 96.6% of the expected hymenopteran orthologs. We also predicted 169,371 repetitive genomic components, 2083 putative transposable elements, and 1946 genes for non-coding RNAs, largely long non-coding RNAs. The mitochondrial genome comprises 15,144 bp, encoding 13 proteins, 22 tRNAs and 2 rRNAs. We observed considerable rearrangement in the mitochondrial gene order compared to other bees. For an in-depth analysis of genes related to social biology, we manually checked the annotations for 533 automatically predicted gene models, including 127 genes related to reproductive processes, 104 to development, and 174 immunity-related genes. We also performed specific searches for genes containing transcription factor domains and genes related to neurogenesis and chemosensory communication. CONCLUSIONS The total genome size for F. varia is similar to the sequenced genomes of other bees. Using specific prediction methods, we identified a large number of repetitive genome components and long non-coding RNAs, which could provide the molecular basis for gene regulatory plasticity, including worker reproduction. The remarkable reshuffling in gene order in the mitochondrial genome suggests that stingless bees may be a hotspot for mtDNA evolution. Hence, while being just the second stingless bee genome sequenced, we expect that subsequent targeting of a selected set of species from this diverse clade of highly eusocial bees will reveal relevant evolutionary signals and trends related to eusociality in these important pollinators.
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Affiliation(s)
- Flávia C. de Paula Freitas
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP Brazil
- Departamento de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, Alfenas, MG Brazil
| | - Anete P. Lourenço
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP Brazil
- Departamento de Ciências Biológicas, Faculdade de Ciências Biológicas e da Saúde, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Diamantina, MG Brazil
| | - Francis M. F. Nunes
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP Brazil
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, SP Brazil
| | | | - Fabiano C. P. Abreu
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP Brazil
| | - Fábio O. Barbin
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP Brazil
| | - Luana Bataglia
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP Brazil
| | - Carlos A. M. Cardoso-Júnior
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, SP 14049-900 Brazil
| | - Mário S. Cervoni
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, SP 14049-900 Brazil
| | - Saura R. Silva
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Jaboticabal, SP Brazil
| | - Fernanda Dalarmi
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP Brazil
| | - Marco A. Del Lama
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, SP Brazil
| | - Thiago S. Depintor
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP Brazil
| | - Kátia M. Ferreira
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, SP Brazil
| | - Paula S. Gória
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, SP Brazil
| | - Michael C. Jaskot
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, SP Brazil
| | - Denyse C. Lago
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP Brazil
| | - Danielle Luna-Lucena
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP Brazil
| | - Livia M. Moda
- Departamento de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, Alfenas, MG Brazil
| | - Leonardo Nascimento
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP Brazil
| | - Matheus Pedrino
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, SP Brazil
| | - Franciene Rabiço Oliveira
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP Brazil
| | - Fernanda C. Sanches
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP Brazil
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, SP Brazil
| | - Douglas E. Santos
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, SP 14049-900 Brazil
| | - Carolina G. Santos
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, SP 14049-900 Brazil
| | - Joseana Vieira
- Departamento de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, Alfenas, MG Brazil
| | - Angel R. Barchuk
- Departamento de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, Alfenas, MG Brazil
| | - Klaus Hartfelder
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, SP 14049-900 Brazil
| | - Zilá L. P. Simões
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP Brazil
| | - Márcia M. G. Bitondi
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP Brazil
| | - Daniel G. Pinheiro
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Jaboticabal, SP Brazil
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8
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Silva SR, Pinheiro DG, Penha HA, Płachno BJ, Michael TP, Meer EJ, Miranda VFO, Varani AM. Intraspecific Variation within the Utricularia amethystina Species Morphotypes Based on Chloroplast Genomes. Int J Mol Sci 2019; 20:E6130. [PMID: 31817365 PMCID: PMC6940893 DOI: 10.3390/ijms20246130] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 11/09/2019] [Accepted: 11/27/2019] [Indexed: 01/09/2023] Open
Abstract
Utricularia amethystina Salzm. ex A.St.-Hil. & Girard (Lentibulariaceae) is a highly polymorphic carnivorous plant taxonomically rearranged many times throughout history. Herein, the complete chloroplast genomes (cpDNA) of three U. amethystina morphotypes: purple-, white-, and yellow-flowered, were sequenced, compared, and putative markers for systematic, populations, and evolutionary studies were uncovered. In addition, RNA-Seq and RNA-editing analysis were employed for functional cpDNA evaluation. The cpDNA of three U. amethystina morphotypes exhibits typical quadripartite structure. Fine-grained sequence comparison revealed a high degree of intraspecific genetic variability in all morphotypes, including an exclusive inversion in the psbM and petN genes in U. amethystina yellow. Phylogenetic analyses indicate that U. amethystina morphotypes are monophyletic. Furthermore, in contrast to the terrestrial Utricularia reniformis cpDNA, the U. amethystina morphotypes retain all the plastid NAD(P)H-dehydrogenase (ndh) complex genes. This observation supports the hypothesis that the ndhs in terrestrial Utricularia were independently lost and regained, also suggesting that different habitats (aquatic and terrestrial) are not related to the absence of Utricularia ndhs gene repertoire as previously assumed. Moreover, RNA-Seq analyses recovered similar patterns, including nonsynonymous RNA-editing sites (e.g., rps14 and petB). Collectively, our results bring new insights into the chloroplast genome architecture and evolution of the photosynthesis machinery in the Lentibulariaceae.
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Affiliation(s)
- Saura R. Silva
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Universidade Estadual Paulista (Unesp), Sao Paulo 14884-900, Brazil; (D.G.P.); (H.A.P.)
| | - Daniel G. Pinheiro
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Universidade Estadual Paulista (Unesp), Sao Paulo 14884-900, Brazil; (D.G.P.); (H.A.P.)
| | - Helen A. Penha
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Universidade Estadual Paulista (Unesp), Sao Paulo 14884-900, Brazil; (D.G.P.); (H.A.P.)
| | - Bartosz J. Płachno
- Department of Plant Cytology and Embryology, Institute of Botany, Faculty of Biology, Jagiellonian University in Kraków, 30-387 Krakow, Poland;
| | | | | | - Vitor F. O. Miranda
- Departamento de Biologia Aplicada à Agropecuária, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Universidade Estadual Paulista (Unesp), Sao Paulo 14884-900, Brazil
| | - Alessandro M. Varani
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Universidade Estadual Paulista (Unesp), Sao Paulo 14884-900, Brazil; (D.G.P.); (H.A.P.)
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9
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Falcon T, Pinheiro DG, Ferreira-Caliman MJ, Turatti ICC, de Abreu FCP, Galaschi-Teixeira JS, Martins JR, Elias-Neto M, Soares MPM, Laure MB, Figueiredo VLC, Lopes NP, Simões ZLP, Garófalo CA, Bitondi MMG. Exploring integument transcriptomes, cuticle ultrastructure, and cuticular hydrocarbons profiles in eusocial and solitary bee species displaying heterochronic adult cuticle maturation. PLoS One 2019; 14:e0213796. [PMID: 30870522 PMCID: PMC6417726 DOI: 10.1371/journal.pone.0213796] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 02/28/2019] [Indexed: 12/26/2022] Open
Abstract
Differences in the timing of exoskeleton melanization and sclerotization are evident when comparing eusocial and solitary bees. This cuticular maturation heterochrony may be associated with life style, considering that eusocial bees remain protected inside the nest for many days after emergence, while the solitary bees immediately start outside activities. To address this issue, we characterized gene expression using large-scale RNA sequencing (RNA-seq), and quantified cuticular hydrocarbon (CHC) through gas chromatography-mass spectrometry in comparative studies of the integument (cuticle plus its underlying epidermis) of two eusocial and a solitary bee species. In addition, we used transmission electron microscopy (TEM) for studying the developing cuticle of these and other three bee species also differing in life style. We found 13,200, 55,209 and 30,161 transcript types in the integument of the eusocial Apis mellifera and Frieseomelitta varia, and the solitary Centris analis, respectively. In general, structural cuticle proteins and chitin-related genes were upregulated in pharate-adults and newly-emerged bees whereas transcripts for odorant binding proteins, cytochrome P450 and antioxidant proteins were overrepresented in foragers. Consistent with our hypothesis, a distance correlation analysis based on the differentially expressed genes suggested delayed cuticle maturation in A. mellifera in comparison to the solitary bee. However, this was not confirmed in the comparison with F. varia. The expression profiles of 27 of 119 genes displaying functional attributes related to cuticle formation/differentiation were positively correlated between A. mellifera and F. varia, and negatively or non-correlated with C. analis, suggesting roles in cuticular maturation heterochrony. However, we also found transcript profiles positively correlated between each one of the eusocial species and C. analis. Gene co-expression networks greatly differed between the bee species, but we identified common gene interactions exclusively between the eusocial species. Except for F. varia, the TEM analysis is consistent with cuticle development timing adapted to the social or solitary life style. In support to our hypothesis, the absolute quantities of n-alkanes and unsaturated CHCs were significantly higher in foragers than in the earlier developmental phases of the eusocial bees, but did not discriminate newly-emerged from foragers in C. analis. By highlighting differences in integument gene expression, cuticle ultrastructure, and CHC profiles between eusocial and solitary bees, our data provided insights into the process of heterochronic cuticle maturation associated to the way of life.
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Affiliation(s)
- Tiago Falcon
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- Núcleo de Bioinformática, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Daniel G. Pinheiro
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Jaboticabal, Brazil
| | - Maria Juliana Ferreira-Caliman
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Izabel C. C. Turatti
- Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Fabiano C. Pinto de Abreu
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Juliana S. Galaschi-Teixeira
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Juliana R. Martins
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Moysés Elias-Neto
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Michelle P. M. Soares
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Marcela B. Laure
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Vera L. C. Figueiredo
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Norberto Peporine Lopes
- Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Zilá L. P. Simões
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Carlos A. Garófalo
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Márcia M. G. Bitondi
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
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10
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Omori WP, Pinheiro DG, Kishi LT, Fernandes CC, Fernandes GC, Gomes-Pepe ES, Pavani CD, Lemos EGDM, Souza JAMD. Draft genome of Thermomonospora sp. CIT 1 (Thermomonosporaceae) and in silico evidence of its functional role in filter cake biomass deconstruction. Genet Mol Biol 2019; 42:145-150. [PMID: 30856245 PMCID: PMC6428131 DOI: 10.1590/1678-4685-gmb-2017-0376] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 06/10/2018] [Indexed: 02/06/2023] Open
Abstract
The filter cake from sugar cane processing is rich in organic matter and nutrients, which favors the proliferation of microorganisms with potential to deconstruct plant biomass. From the metagenomic data of this material, we assembled a draft genome that was phylogenetically related to Thermomonospora curvata DSM 43183, which shows the functional and ecological importance of this bacterium in the filter cake. Thermomonospora is a gram-positive bacterium that produces cellulases in compost, and it can survive temperatures of 60 ºC. We identified a complete set of biomass depolymerizing enzymes in the draft genome of Thermomonospora sp. CIT 1, such as α-amylase, catalase-peroxidases, β-mannanase, and arabinanase, demonstrating the potential of this bacterium to deconstruct the components of starch, lignin, and hemicellulose. In addition, the draft genome of Thermomonospora sp. CIT 1 contains 18 genes that do not share identity with five other species of Thermomonospora, suggesting that this bacterium has different genetic characteristics than those present in genomes reported so far for this genus. These findings add a new dimension to the current understanding of the functional profile of this microorganism that inhabits agro-industrial waste, which may boost new gene discoveries and be of importance for application in the production of bioethanol.
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Affiliation(s)
- Wellington P Omori
- Programa de Pós-Graduação em Microbiologia Agropecuária, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal, SP, Brazil
| | - Daniel G Pinheiro
- Departamento de Tecnologia, Laboratório de Bioinformática, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal, SP, Brazil
| | - Luciano T Kishi
- Laboratório Multiusuário Centralizado para Sequenciamento de DNA em Larga Escala e Análise de Expressão Gênica (LMSeq), Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal, SP, Brazil
| | - Camila C Fernandes
- Laboratório Multiusuário Centralizado para Sequenciamento de DNA em Larga Escala e Análise de Expressão Gênica (LMSeq), Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal, SP, Brazil
| | - Gabriela C Fernandes
- Programa de Pós-Graduação em Microbiologia Agropecuária, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal, SP, Brazil
| | - Elisângela S Gomes-Pepe
- Laboratório Multiusuário Centralizado para Sequenciamento de DNA em Larga Escala e Análise de Expressão Gênica (LMSeq), Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal, SP, Brazil
| | - Claudio D Pavani
- Programa de Pós-Graduação em Microbiologia Agropecuária, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal, SP, Brazil
| | - Eliana G de M Lemos
- Laboratório Multiusuário Centralizado para Sequenciamento de DNA em Larga Escala e Análise de Expressão Gênica (LMSeq), Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal, SP, Brazil
| | - Jackson A M de Souza
- Departamento de Biologia Aplicada à Agropecuária, Laboratório de Genética Aplicada, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal, SP, Brazil
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11
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Mello TRP, Aleixo AC, Pinheiro DG, Nunes FMF, Cristino AS, Bitondi MMG, Barchuk AR, Simões ZLP. Hormonal control and target genes of ftz-f1 expression in the honeybee Apis mellifera: a positive loop linking juvenile hormone, ftz-f1, and vitellogenin. Insect Mol Biol 2019; 28:145-159. [PMID: 30270498 DOI: 10.1111/imb.12541] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Ftz-f1 is an orphan member of the nuclear hormone receptor superfamily. A 20-hydroxyecdysone pulse allows ftz-f1 gene expression, which then regulates the activity of downstream genes involved in major developmental progression events. In honeybees, the expression of genes like vitellogenin (vg), prophenoloxidase and juvenile hormone-esterase during late pharate-adult development is known to be hormonally controlled in both queens and workers by increasing juvenile hormone (JH) titres in the presence of declining levels of ecdysteroids. Since Ftz-f1 is known for mediating intracellular JH signalling, we hypothesized that ftz-f1 could mediate JH action during the pharate-adult development of honeybees, thus controlling the expression of these genes. Here, we show that ftz-f1 has caste-specific transcription profiles during this developmental period, with a peak coinciding with the increase in JH titre, and that its expression is upregulated by JH and downregulated by ecdysteroids. RNAi-mediated knock down of ftz-f1 showed that the expression of genes essential for adult development (e.g. vg and cuticular genes) depends on ftz-f1 expression. Finally, a double-repressor hypothesis-inspired vg gene knock-down experiment suggests the existence of a positive molecular loop between JH, ftz-f1 and vg.
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Affiliation(s)
- T R P Mello
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - A C Aleixo
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - D G Pinheiro
- Faculdade de Ciências Agrárias e Veterinárias, UNESP - Universidade Estadual Paulista, Jaboticabal, São Paulo, Brazil
| | - F M F Nunes
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - A S Cristino
- Translational Research Institute, The University of Queensland Diamantina Institute, Brisbane, Australia
| | - M M G Bitondi
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - A R Barchuk
- Departamento de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, UNIFAL-MG, Alfenas, Minas Gerais, Brazil
| | - Z L P Simões
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
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12
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Silva SR, Michael TP, Meer EJ, Pinheiro DG, Varani AM, Miranda VFO. Comparative genomic analysis of Genlisea (corkscrew plants-Lentibulariaceae) chloroplast genomes reveals an increasing loss of the ndh genes. PLoS One 2018; 13:e0190321. [PMID: 29293597 PMCID: PMC5749785 DOI: 10.1371/journal.pone.0190321] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 12/12/2017] [Indexed: 11/18/2022] Open
Abstract
In the carnivorous plant family Lentibulariaceae, all three genome compartments (nuclear, chloroplast, and mitochondria) have some of the highest rates of nucleotide substitutions across angiosperms. While the genera Genlisea and Utricularia have the smallest known flowering plant nuclear genomes, the chloroplast genomes (cpDNA) are mostly structurally conserved except for deletion and/or pseudogenization of the NAD(P)H-dehydrogenase complex (ndh) genes known to be involved in stress conditions of low light or CO2 concentrations. In order to determine how the cpDNA are changing, and to better understand the evolutionary history within the Genlisea genus, we sequenced, assembled and analyzed complete cpDNA from six species (G. aurea, G. filiformis, G. pygmaea, G. repens, G. tuberosa and G. violacea) together with the publicly available G. margaretae cpDNA. In general, the cpDNA structure among the analyzed Genlisea species is highly similar. However, we found that the plastidial ndh genes underwent a progressive process of degradation similar to the other terrestrial Lentibulariaceae cpDNA analyzed to date, but in contrast to the aquatic species. Contrary to current thinking that the terrestrial environment is a more stressful environment and thus requiring the ndh genes, we provide evidence that in the Lentibulariaceae the terrestrial forms have progressive loss while the aquatic forms have the eleven plastidial ndh genes intact. Therefore, the Lentibulariaceae system provides an important opportunity to understand the evolutionary forces that govern the transition to an aquatic environment and may provide insight into how plants manage water stress at a genome scale.
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Affiliation(s)
- Saura R. Silva
- Universidade Estadual Paulista (Unesp), Botucatu, Instituto de Biociências, São Paulo, Brazil
| | - Todd P. Michael
- J. Craig Venter Institute, La Jolla, CA, United States of America
| | - Elliott J. Meer
- 10X Genomics, Pleasanton, California, United States of America
| | - Daniel G. Pinheiro
- Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Departamento de Tecnologia, São Paulo, Brazil
| | - Alessandro M. Varani
- Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Departamento de Tecnologia, São Paulo, Brazil
| | - Vitor F. O. Miranda
- Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Departamento de Biologia Aplicada à Agropecuária, São Paulo, Brazil
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13
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Silva SR, Alvarenga DO, Aranguren Y, Penha HA, Fernandes CC, Pinheiro DG, Oliveira MT, Michael TP, Miranda VFO, Varani AM. The mitochondrial genome of the terrestrial carnivorous plant Utricularia reniformis (Lentibulariaceae): Structure, comparative analysis and evolutionary landmarks. PLoS One 2017; 12:e0180484. [PMID: 28723946 PMCID: PMC5516982 DOI: 10.1371/journal.pone.0180484] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 05/13/2017] [Indexed: 11/18/2022] Open
Abstract
The carnivorous plants of the family Lentibulariaceae have attained recent attention not only because of their interesting lifestyle, but also because of their dynamic nuclear genome size. Lentibulariaceae genomes span an order of magnitude and include species with the smallest genomes in angiosperms, making them a powerful system to study the mechanisms of genome expansion and contraction. However, little is known about mitochondrial DNA (mtDNA) sequences of this family, and the evolutionary forces that shape this organellar genome. Here we report the sequencing and assembly of the complete mtDNA from the endemic terrestrial Brazilian species Utricularia reniformis. The 857,234bp master circle mitochondrial genome encodes 70 transcriptionaly active genes (42 protein-coding, 25 tRNAs and 3 rRNAs), covering up to 7% of the mtDNA. A ltrA-like protein related to splicing and mobility and a LAGLIDADG homing endonuclease have been identified in intronic regions, suggesting particular mechanisms of genome maintenance. RNA-seq analysis identified properties with putative diverse and important roles in genome regulation and evolution: 1) 672kbp (78%) of the mtDNA is covered by full-length reads; 2) most of the 243kbp intergenic regions exhibit transcripts; and 3) at least 69 novel RNA editing sites in the protein-coding genes. Additional genomic features are hypothetical ORFs (48%), chloroplast insertions, including truncated plastid genes that have been lost from the chloroplast DNA (5%), repeats (5%), relics of transposable elements mostly related to LTR retrotransposons (5%), and truncated mitovirus sequences (0.4%). Phylogenetic analysis based on 32 different Lamiales mitochondrial genomes corroborate that Lentibulariaceae is a monophyletic group. In summary, the U. reniformis mtDNA represents the eighth largest plant mtDNA described to date, shedding light on the genomic trends and evolutionary characteristics and phylogenetic history of the family Lentibulariaceae.
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Affiliation(s)
- Saura R. Silva
- Departamento de Botânica, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, São Paulo, Brazil
| | - Danillo O. Alvarenga
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (Unesp), Jaboticabal, São Paulo, Brazil
| | - Yani Aranguren
- Departamento de Biologia Aplicada à Agropecuária, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (Unesp), Jaboticabal, São Paulo, Brazil
| | - Helen A. Penha
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (Unesp), Jaboticabal, São Paulo, Brazil
| | - Camila C. Fernandes
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (Unesp), Jaboticabal, São Paulo, Brazil
| | - Daniel G. Pinheiro
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (Unesp), Jaboticabal, São Paulo, Brazil
| | - Marcos T. Oliveira
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (Unesp), Jaboticabal, São Paulo, Brazil
| | - Todd P. Michael
- Computational Genomics, Ibis Bioscience, Carlsbad, CA, United States of America
| | - Vitor F. O. Miranda
- Departamento de Biologia Aplicada à Agropecuária, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (Unesp), Jaboticabal, São Paulo, Brazil
| | - Alessandro M. Varani
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (Unesp), Jaboticabal, São Paulo, Brazil
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14
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Belesini AA, Carvalho FMS, Telles BR, de Castro GM, Giachetto PF, Vantini JS, Carlin SD, Cazetta JO, Pinheiro DG, Ferro MIT. De novo transcriptome assembly of sugarcane leaves submitted to prolonged water-deficit stress. Genet Mol Res 2017; 16:gmr-16-02-gmr.16028845. [PMID: 28549198 DOI: 10.4238/gmr16028845] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Sugarcane production is strongly influenced by drought, which is a limiting factor for agricultural productivity in the world. In this study, the gene expression profiles obtained by de novo assembly of the leaf transcriptome of two sugarcane cultivars that differ in their physiological response to water deficit were evaluated by the RNA-Seq method: drought-tolerant cultivar (SP81-3250) and drought-sensitive cultivar (RB855453). For this purpose, plants were grown in a greenhouse for 60 days and were then submitted to three treatments: control (-0.01 to -0.015 MPa), moderate water deficit (-0.05 to -0.055 MPa), and severe water deficit (-0.075 to -0.08 MPa). The plants were evaluated 30, 60, and 90 days after the beginning of treatment. Sequencing on an Illumina platform (RNA-Seq) generated more than one billion sequences, resulting in 177,509 and 185,153 transcripts for the tolerant and sensitive cultivar, respectively. These transcripts were aligned with sequences from Saccharum spp, Sorghum bicolor, Miscanthus giganteus, and Arabidopsis thaliana available in public databases. The differentially expressed genes detected during the prolonged period of water deficit permit to increase our understanding of the molecular patterns involved in the physiological response of the two cultivars. The tolerant cultivar differentially expressed a larger number of genes at 90 days, while in the sensitive cultivar the number of differentially expressed genes was higher in 30 days. Both cultivars perceived the lack of water, but the tolerant cultivar responded more slowly than the sensitive cultivar. The latter requires rapid activation of different water-deficit stress response mechanisms for its survival. This rapid activation of metabolic pathways in response to water stress does not appear to be the key mechanism of drought tolerance in sugarcane. There is still much to clarify on the molecular and physiological pattern of plants in response to drought.
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Affiliation(s)
- A A Belesini
- Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Departamento de Tecnologia, Jaboticabal, SP, Brasil
| | - F M S Carvalho
- Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Departamento de Tecnologia, Jaboticabal, SP, Brasil
| | - B R Telles
- Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Departamento de Tecnologia, Jaboticabal, SP, Brasil
| | | | | | - J S Vantini
- Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Departamento de Engenharia Rural, Jaboticabal, SP, Brasil
| | | | - J O Cazetta
- Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Departamento de Tecnologia, Jaboticabal, SP, Brasil
| | - D G Pinheiro
- Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Departamento de Tecnologia, Jaboticabal, SP, Brasil
| | - M I T Ferro
- Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Departamento de Tecnologia, Jaboticabal, SP, Brasil
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15
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Silva SR, Pinheiro DG, Meer EJ, Michael TP, Varani AM, Miranda VFO. The complete chloroplast genome sequence of the leafy bladderwort, Utricularia foliosa L. (Lentibulariaceae). CONSERV GENET RESOUR 2016. [DOI: 10.1007/s12686-016-0653-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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16
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Silva SR, Diaz YCA, Penha HA, Pinheiro DG, Fernandes CC, Miranda VFO, Michael TP, Varani AM. The Chloroplast Genome of Utricularia reniformis Sheds Light on the Evolution of the ndh Gene Complex of Terrestrial Carnivorous Plants from the Lentibulariaceae Family. PLoS One 2016; 11:e0165176. [PMID: 27764252 PMCID: PMC5072713 DOI: 10.1371/journal.pone.0165176] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 10/08/2016] [Indexed: 02/06/2023] Open
Abstract
Lentibulariaceae is the richest family of carnivorous plants spanning three genera including Pinguicula, Genlisea, and Utricularia. Utricularia is globally distributed, and, unlike Pinguicula and Genlisea, has both aquatic and terrestrial forms. In this study we present the analysis of the chloroplast (cp) genome of the terrestrial Utricularia reniformis. U. reniformis has a standard cp genome of 139,725bp, encoding a gene repertoire similar to essentially all photosynthetic organisms. However, an exclusive combination of losses and pseudogenization of the plastid NAD(P)H-dehydrogenase (ndh) gene complex were observed. Comparisons among aquatic and terrestrial forms of Pinguicula, Genlisea, and Utricularia indicate that, whereas the aquatic forms retained functional copies of the eleven ndh genes, these have been lost or truncated in terrestrial forms, suggesting that the ndh function may be dispensable in terrestrial Lentibulariaceae. Phylogenetic scenarios of the ndh gene loss and recovery among Pinguicula, Genlisea, and Utricularia to the ancestral Lentibulariaceae cladeare proposed. Interestingly, RNAseq analysis evidenced that U. reniformis cp genes are transcribed, including the truncated ndh genes, suggesting that these are not completely inactivated. In addition, potential novel RNA-editing sites were identified in at least six U. reniformis cp genes, while none were identified in the truncated ndh genes. Moreover, phylogenomic analyses support that Lentibulariaceae is monophyletic, belonging to the higher core Lamiales clade, corroborating the hypothesis that the first Utricularia lineage emerged in terrestrial habitats and then evolved to epiphytic and aquatic forms. Furthermore, several truncated cp genes were found interspersed with U. reniformis mitochondrial and nuclear genome scaffolds, indicating that as observed in other smaller plant genomes, such as Arabidopsis thaliana, and the related and carnivorous Genlisea nigrocaulis and G. hispidula, the endosymbiotic gene transfer may also shape the U. reniformis genome in a similar fashion. Overall the comparative analysis of the U. reniformis cp genome provides new insight into the ndh genes and cp genome evolution of carnivorous plants from Lentibulariaceae family.
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Affiliation(s)
- Saura R. Silva
- Instituto de Biociências, UNESP - Univ Estadual Paulista, Câmpus Botucatu, São Paulo, Brazil
| | - Yani C. A. Diaz
- Departamento de Biologia Aplicada à Agropecuária, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista, Câmpus Jaboticabal, São Paulo, Brazil
| | - Helen Alves Penha
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista, Câmpus Jaboticabal, São Paulo, Brazil
| | - Daniel G. Pinheiro
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista, Câmpus Jaboticabal, São Paulo, Brazil
| | - Camila C. Fernandes
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista, Câmpus Jaboticabal, São Paulo, Brazil
| | - Vitor F. O. Miranda
- Departamento de Biologia Aplicada à Agropecuária, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista, Câmpus Jaboticabal, São Paulo, Brazil
| | - Todd P. Michael
- Ibis Bioscience, Computational Genomics, Carlsbad, California, United States of America
| | - Alessandro M. Varani
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista, Câmpus Jaboticabal, São Paulo, Brazil
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17
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de Lima KA, de Oliveira GLV, Yaochite JNU, Pinheiro DG, de Azevedo JTC, Silva WA, Covas DT, Couri CEB, Simões BP, Voltarelli JC, Oliveira MC, Malmegrim KCR. Transcriptional profiling reveals intrinsic mRNA alterations in multipotent mesenchymal stromal cells isolated from bone marrow of newly-diagnosed type 1 diabetes patients. Stem Cell Res Ther 2016; 7:92. [PMID: 27406064 PMCID: PMC4942931 DOI: 10.1186/s13287-016-0351-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 04/12/2016] [Accepted: 06/22/2016] [Indexed: 02/07/2023] Open
Abstract
Background Bone marrow multipotent mesenchymal stromal cells (MSCs) are a diverse subset of precursors that contribute to the homeostasis of the hematopoietic niche. MSCs can be isolated and expanded in vitro and have unique immunomodulatory and regenerative properties that make them attractive for the treatment of autoimmune diseases, including type 1 diabetes (T1D). Whether autologous or allogeneic MSCs are more suitable for therapeutic purposes has not yet been established. While autologous MSCs may present abnormal function, allogeneic cells may be recognized and rejected by the host immune system. Thus, studies that investigate biological characteristics of MSCs isolated from T1D patients are essential to guide future clinical applications. Methods Bone marrow-derived MSCs from recently diagnosed type 1 diabetes patients (T1D-MSCs) were compared with those from healthy individuals (C-MSCs) for morphological and immunophenotypic characteristics and for differentiation potential. Bioinformatics approaches allowed us to match absolute and differential gene expression of several adhesion molecules, immune mediators, growth factors, and their receptors involved with hematopoietic support and immunomodulatory properties of MSCs. Finally, the differentially expressed genes were collated for functional pathway enrichment analysis. Results T1D-MSCs and C-MSCs were similar for morphology, immunophenotype, and differentiation potential. Our absolute gene expression results supported previous literature reports, while also detecting new potential molecules related to bone marrow-derived MSC functions. T1D-MSCs showed intrinsic abnormalities in mRNA expression, including the immunomodulatory molecules VCAM-1, CXCL12, HGF, and CCL2. Pathway analyses revealed activation of sympathetic nervous system and JAK STAT signaling in T1D-MSCs. Conclusions Collectively, our results indicate that MSCs isolated from T1D patients present intrinsic transcriptional alterations that may affect their therapeutic potential. However, the implications of these abnormalities in T1D development as well as in the therapeutic efficacy of autologous MSCs require further investigation. Electronic supplementary material The online version of this article (doi:10.1186/s13287-016-0351-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kalil A de Lima
- Center for Cell-Based Research, Regional Blood Center of Ribeirao Preto, Ribeirao Preto Medical, University of Sao Paulo, Ribeirao Preto, Brazil. .,Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Brazil. .,, Tenente Catao Roxo, 2501, Monte Alegre, 14051-140, Ribeirao Preto, Sao Paulo, Brazil.
| | - Gislane L V de Oliveira
- Center for Cell-Based Research, Regional Blood Center of Ribeirao Preto, Ribeirao Preto Medical, University of Sao Paulo, Ribeirao Preto, Brazil.,Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Juliana N U Yaochite
- Center for Cell-Based Research, Regional Blood Center of Ribeirao Preto, Ribeirao Preto Medical, University of Sao Paulo, Ribeirao Preto, Brazil.,Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Brazil.,Department of Clinical and Toxicological Analysis, Federal University of Ceará, Fortaleza, Ceara, Brazil
| | - Daniel G Pinheiro
- Center for Cell-Based Research, Regional Blood Center of Ribeirao Preto, Ribeirao Preto Medical, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Júlia T C de Azevedo
- Center for Cell-Based Research, Regional Blood Center of Ribeirao Preto, Ribeirao Preto Medical, University of Sao Paulo, Ribeirao Preto, Brazil.,Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Wilson Araujo Silva
- Center for Cell-Based Research, Regional Blood Center of Ribeirao Preto, Ribeirao Preto Medical, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Dimas T Covas
- Center for Cell-Based Research, Regional Blood Center of Ribeirao Preto, Ribeirao Preto Medical, University of Sao Paulo, Ribeirao Preto, Brazil.,Department of Clinical Medicine, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Carlos E B Couri
- Center for Cell-Based Research, Regional Blood Center of Ribeirao Preto, Ribeirao Preto Medical, University of Sao Paulo, Ribeirao Preto, Brazil.,Department of Clinical Medicine, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Belinda P Simões
- Center for Cell-Based Research, Regional Blood Center of Ribeirao Preto, Ribeirao Preto Medical, University of Sao Paulo, Ribeirao Preto, Brazil.,Department of Clinical Medicine, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Julio C Voltarelli
- Center for Cell-Based Research, Regional Blood Center of Ribeirao Preto, Ribeirao Preto Medical, University of Sao Paulo, Ribeirao Preto, Brazil.,Department of Clinical Medicine, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Maria C Oliveira
- Center for Cell-Based Research, Regional Blood Center of Ribeirao Preto, Ribeirao Preto Medical, University of Sao Paulo, Ribeirao Preto, Brazil.,Department of Clinical Medicine, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Kelen C R Malmegrim
- Center for Cell-Based Research, Regional Blood Center of Ribeirao Preto, Ribeirao Preto Medical, University of Sao Paulo, Ribeirao Preto, Brazil.,Department of Clinical, Toxicological and Bromatological Analysis, Faculty of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Brazil
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18
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Macedo LMF, Nunes FMF, Freitas FCP, Pires CV, Tanaka ED, Martins JR, Piulachs MD, Cristino AS, Pinheiro DG, Simões ZLP. MicroRNA signatures characterizing caste-independent ovarian activity in queen and worker honeybees (Apis mellifera L.). Insect Mol Biol 2016; 25:216-26. [PMID: 26853694 DOI: 10.1111/imb.12214] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Queen and worker honeybees differ profoundly in reproductive capacity. The queen of this complex society, with 200 highly active ovarioles in each ovary, is the fertile caste, whereas the workers have approximately 20 ovarioles as a result of receiving a different diet during larval development. In a regular queenright colony, the workers have inactive ovaries and do not reproduce. However, if the queen is sensed to be absent, some of the workers activate their ovaries, producing viable haploid eggs that develop into males. Here, a deep-sequenced ovary transcriptome library of reproductive workers was used as supporting data to assess the dynamic expression of the regulatory molecules and microRNAs (miRNAs) of reproductive and nonreproductive honeybee females. In this library, most of the differentially expressed miRNAs are related to ovary physiology or oogenesis. When we quantified the dynamic expression of 19 miRNAs in the active and inactive worker ovaries and compared their expression in the ovaries of virgin and mated queens, we noted that some miRNAs (miR-1, miR-31a, miR-13b, miR-125, let-7 RNA, miR-100, miR-276, miR-12, miR-263a, miR-306, miR-317, miR-92a and miR-9a) could be used to identify reproductive and nonreproductive statuses independent of caste. Furthermore, integrative gene networks suggested that some candidate miRNAs function in the process of ovary activation in worker bees.
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Affiliation(s)
- L M F Macedo
- Departamento De Genética, Faculdade De Medicina De Ribeirão Preto, Universidade De São Paulo, Ribeirão Preto, Brazil
| | - F M F Nunes
- Departamento De Genética E Evolução, Centro De Ciências Biológicas E Da Saúde, Universidade Federal De São Carlos, São Carlos, Brazil
| | - F C P Freitas
- Departamento De Genética, Faculdade De Medicina De Ribeirão Preto, Universidade De São Paulo, Ribeirão Preto, Brazil
| | - C V Pires
- Departamento De Genética, Faculdade De Medicina De Ribeirão Preto, Universidade De São Paulo, Ribeirão Preto, Brazil
| | - E D Tanaka
- Departamento De Genética, Faculdade De Medicina De Ribeirão Preto, Universidade De São Paulo, Ribeirão Preto, Brazil
| | - J R Martins
- Departamento De Genética, Faculdade De Medicina De Ribeirão Preto, Universidade De São Paulo, Ribeirão Preto, Brazil
| | - M-D Piulachs
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - A S Cristino
- The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Australia
| | - D G Pinheiro
- Departamento De Tecnologia, Faculdade De Ciências Agrárias E Veterinárias, Universidade Estadual Paulista, Jaboticabal, Brazil
| | - Z L P Simões
- Departamento De Biologia, Faculdade De Filosofia, Ciências E Letras De Ribeirão Preto, Universidade De São Paulo, Ribeirão Preto, Brazil
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19
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Sadd BM, Barribeau SM, Bloch G, de Graaf DC, Dearden P, Elsik CG, Gadau J, Grimmelikhuijzen CJP, Hasselmann M, Lozier JD, Robertson HM, Smagghe G, Stolle E, Van Vaerenbergh M, Waterhouse RM, Bornberg-Bauer E, Klasberg S, Bennett AK, Câmara F, Guigó R, Hoff K, Mariotti M, Munoz-Torres M, Murphy T, Santesmasses D, Amdam GV, Beckers M, Beye M, Biewer M, Bitondi MMG, Blaxter ML, Bourke AFG, Brown MJF, Buechel SD, Cameron R, Cappelle K, Carolan JC, Christiaens O, Ciborowski KL, Clarke DF, Colgan TJ, Collins DH, Cridge AG, Dalmay T, Dreier S, du Plessis L, Duncan E, Erler S, Evans J, Falcon T, Flores K, Freitas FCP, Fuchikawa T, Gempe T, Hartfelder K, Hauser F, Helbing S, Humann FC, Irvine F, Jermiin LS, Johnson CE, Johnson RM, Jones AK, Kadowaki T, Kidner JH, Koch V, Köhler A, Kraus FB, Lattorff HMG, Leask M, Lockett GA, Mallon EB, Antonio DSM, Marxer M, Meeus I, Moritz RFA, Nair A, Näpflin K, Nissen I, Niu J, Nunes FMF, Oakeshott JG, Osborne A, Otte M, Pinheiro DG, Rossié N, Rueppell O, Santos CG, Schmid-Hempel R, Schmitt BD, Schulte C, Simões ZLP, Soares MPM, Swevers L, Winnebeck EC, Wolschin F, Yu N, Zdobnov EM, Aqrawi PK, Blankenburg KP, Coyle M, Francisco L, Hernandez AG, Holder M, Hudson ME, Jackson L, Jayaseelan J, Joshi V, Kovar C, Lee SL, Mata R, Mathew T, Newsham IF, Ngo R, Okwuonu G, Pham C, Pu LL, Saada N, Santibanez J, Simmons D, Thornton R, Venkat A, Walden KKO, Wu YQ, Debyser G, Devreese B, Asher C, Blommaert J, Chipman AD, Chittka L, Fouks B, Liu J, O'Neill MP, Sumner S, Puiu D, Qu J, Salzberg SL, Scherer SE, Muzny DM, Richards S, Robinson GE, Gibbs RA, Schmid-Hempel P, Worley KC. The genomes of two key bumblebee species with primitive eusocial organization. Genome Biol 2015; 16:76. [PMID: 25908251 PMCID: PMC4414376 DOI: 10.1186/s13059-015-0623-3] [Citation(s) in RCA: 241] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 03/10/2015] [Indexed: 12/25/2022] Open
Abstract
Background The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats. Results We report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens, two ecologically dominant bumblebees and widely utilized study species. Comparing these new genomes to those of the highly eusocial honeybee Apis mellifera and other Hymenoptera, we identify deeply conserved similarities, as well as novelties key to the biology of these organisms. Some honeybee genome features thought to underpin advanced eusociality are also present in bumblebees, indicating an earlier evolution in the bee lineage. Xenobiotic detoxification and immune genes are similarly depauperate in bumblebees and honeybees, and multiple categories of genes linked to social organization, including development and behavior, show high conservation. Key differences identified include a bias in bumblebee chemoreception towards gustation from olfaction, and striking differences in microRNAs, potentially responsible for gene regulation underlying social and other traits. Conclusions These two bumblebee genomes provide a foundation for post-genomic research on these key pollinators and insect societies. Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0623-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ben M Sadd
- School of Biological Sciences, Illinois State University, Normal, IL, 61790, USA. .,Experimental Ecology, Institute of Integrative Biology, Eidgenössiche Technische Hochschule (ETH) Zürich, CH-8092, Zürich, Switzerland.
| | - Seth M Barribeau
- Experimental Ecology, Institute of Integrative Biology, Eidgenössiche Technische Hochschule (ETH) Zürich, CH-8092, Zürich, Switzerland. .,Department of Biology, East Carolina University, Greenville, NC, 27858, USA.
| | - Guy Bloch
- Department of Ecology, Evolution, and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Dirk C de Graaf
- Laboratory of Zoophysiology, Faculty of Sciences, Ghent University, Krijgslaan 281, S2, 9000, Ghent, Belgium.
| | - Peter Dearden
- Laboratory for Evolution and Development, Genetics Otago and the National Research Centre for Growth and Development, Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand.
| | - Christine G Elsik
- Division of Animal Sciences, Division of Plant Sciences, and MU Informatics Institute, University of Missouri, Columbia, MO, 65211, USA. .,Department of Biology, Georgetown University, Washington, DC, 20057, USA.
| | - Jürgen Gadau
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA.
| | - Cornelis J P Grimmelikhuijzen
- Center for Functional and Comparative Insect Genomics, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Martin Hasselmann
- University of Hohenheim, Institute of Animal Science, Garbenstrasse 17, 70599, Stuttgart, Germany.
| | - Jeffrey D Lozier
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, 35487, USA.
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Guy Smagghe
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.
| | - Eckart Stolle
- Institute of Biology, Martin-Luther-University Halle-Wittenberg, Wittenberg, Germany.
| | - Matthias Van Vaerenbergh
- Laboratory of Zoophysiology, Faculty of Sciences, Ghent University, Krijgslaan 281, S2, 9000, Ghent, Belgium.
| | - Robert M Waterhouse
- Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211, Geneva, Switzerland. .,Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211, Geneva, Switzerland. .,Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA, 02139, USA. .,The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA, 02142, USA.
| | - Erich Bornberg-Bauer
- Westfalian Wilhelms University, Institute of Evolution and Biodiversity, Huefferstrasse 1, 48149, Muenster, Germany.
| | - Steffen Klasberg
- Westfalian Wilhelms University, Institute of Evolution and Biodiversity, Huefferstrasse 1, 48149, Muenster, Germany.
| | - Anna K Bennett
- Department of Biology, Georgetown University, Washington, DC, 20057, USA.
| | - Francisco Câmara
- Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain.
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain.
| | - Katharina Hoff
- Ernst Moritz Arndt University Greifswald, Institute for Mathematics and Computer Science, Walther-Rathenau-Str. 47, 17487, Greifswald, Germany.
| | - Marco Mariotti
- Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain.
| | - Monica Munoz-Torres
- Department of Biology, Georgetown University, Washington, DC, 20057, USA. .,Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Terence Murphy
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, USA.
| | - Didac Santesmasses
- Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain.
| | - Gro V Amdam
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA. .,Department of Chemistry, Biotechnology and Food Science, Norwegian University of Food Science, N-1432, Aas, Norway.
| | - Matthew Beckers
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Martin Beye
- Institute of Evolutionary Genetics, Heinrich Heine University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany.
| | - Matthias Biewer
- University of Hohenheim, Institute of Animal Science, Garbenstrasse 17, 70599, Stuttgart, Germany. .,University of Cologne, Institute of Genetics, Cologne, Germany.
| | - Márcia M G Bitondi
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, 14040-901, Ribeirão Preto, Brazil.
| | - Mark L Blaxter
- Institute of Evolutionary Biology and Edinburgh Genomics, The Ashworth Laboratories, The King's Buildings, University of Edinburgh, Edinburgh, EH9 3FL, UK.
| | - Andrew F G Bourke
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Mark J F Brown
- School of Biological Sciences, Royal Holloway University of London, London, UK.
| | - Severine D Buechel
- Experimental Ecology, Institute of Integrative Biology, Eidgenössiche Technische Hochschule (ETH) Zürich, CH-8092, Zürich, Switzerland.
| | - Rossanah Cameron
- Laboratory for Evolution and Development, Genetics Otago and the National Research Centre for Growth and Development, Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand.
| | - Kaat Cappelle
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - James C Carolan
- Maynooth University Department of Biology, Maynooth University, Co, Kildare, Ireland.
| | - Olivier Christiaens
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.
| | - Kate L Ciborowski
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK.
| | | | - Thomas J Colgan
- Department of Zoology, School of Natural Sciences, Trinity College Dublin, Dublin, Ireland.
| | - David H Collins
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Andrew G Cridge
- Laboratory for Evolution and Development, Genetics Otago and the National Research Centre for Growth and Development, Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand.
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Stephanie Dreier
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK.
| | - Louis du Plessis
- Theoretical Biology, Institute of Integrative Biology, Eidgenössiche Technische Hochschule (ETH) Zürich, CH-8092, Zürich, Switzerland. .,Swiss Institute of Bioinformatics, Lausanne, Switzerland. .,Computational Evolution, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
| | - Elizabeth Duncan
- Laboratory for Evolution and Development, Genetics Otago and the National Research Centre for Growth and Development, Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand.
| | - Silvio Erler
- Institute of Biology, Martin-Luther-University Halle-Wittenberg, Wittenberg, Germany.
| | - Jay Evans
- USDA-ARS Bee Research Laboratory, Maryland, USA.
| | - Tiago Falcon
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, 14040-900, Ribeirão Preto, Brazil.
| | - Kevin Flores
- Center for Research in Scientific Computation, North Carolina State University Raleigh, Raleigh, NC, USA.
| | - Flávia C P Freitas
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, 14040-900, Ribeirão Preto, Brazil.
| | - Taro Fuchikawa
- Department of Ecology, Evolution, and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel. .,Laboratory of Insect Ecology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
| | - Tanja Gempe
- Institute of Evolutionary Genetics, Heinrich Heine University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany.
| | - Klaus Hartfelder
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, 14040-900, Ribeirão Preto, Brazil.
| | - Frank Hauser
- Center for Functional and Comparative Insect Genomics, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Sophie Helbing
- Institute of Biology, Martin-Luther-University Halle-Wittenberg, Wittenberg, Germany.
| | - Fernanda C Humann
- Instituto Federal de Educação, Ciência e Tecnologia de São Paulo, 15991-502, Matão, Brazil.
| | - Frano Irvine
- Laboratory for Evolution and Development, Genetics Otago and the National Research Centre for Growth and Development, Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand.
| | | | - Claire E Johnson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Reed M Johnson
- Department of Entomology, The Ohio State University, Wooster, OH, 44791, USA.
| | - Andrew K Jones
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK.
| | - Tatsuhiko Kadowaki
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, China.
| | - Jonathan H Kidner
- Institute of Biology, Martin-Luther-University Halle-Wittenberg, Wittenberg, Germany.
| | - Vasco Koch
- Institute of Evolutionary Genetics, Heinrich Heine University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany.
| | - Arian Köhler
- Institute of Evolutionary Genetics, Heinrich Heine University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany.
| | - F Bernhard Kraus
- Institute of Biology, Martin-Luther-University Halle-Wittenberg, Wittenberg, Germany. .,Department of Laboratory Medicine, University Hospital Halle (Saale), Halle, Germany.
| | - H Michael G Lattorff
- Institute of Biology, Martin-Luther-University Halle-Wittenberg, Wittenberg, Germany. .,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
| | - Megan Leask
- Laboratory for Evolution and Development, Genetics Otago and the National Research Centre for Growth and Development, Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand.
| | | | - Eamonn B Mallon
- Department of Biology, University of Leicester, Leicester, UK.
| | - David S Marco Antonio
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, 14040-900, Ribeirão Preto, Brazil.
| | - Monika Marxer
- Experimental Ecology, Institute of Integrative Biology, Eidgenössiche Technische Hochschule (ETH) Zürich, CH-8092, Zürich, Switzerland.
| | - Ivan Meeus
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.
| | - Robin F A Moritz
- Institute of Biology, Martin-Luther-University Halle-Wittenberg, Wittenberg, Germany.
| | - Ajay Nair
- Laboratory for Evolution and Development, Genetics Otago and the National Research Centre for Growth and Development, Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand.
| | - Kathrin Näpflin
- Experimental Ecology, Institute of Integrative Biology, Eidgenössiche Technische Hochschule (ETH) Zürich, CH-8092, Zürich, Switzerland.
| | - Inga Nissen
- Institute of Evolutionary Genetics, Heinrich Heine University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany.
| | - Jinzhi Niu
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.
| | - Francis M F Nunes
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, 13565-905, São Carlos, Brazil.
| | | | - Amy Osborne
- Laboratory for Evolution and Development, Genetics Otago and the National Research Centre for Growth and Development, Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand.
| | - Marianne Otte
- Institute of Biology, Martin-Luther-University Halle-Wittenberg, Wittenberg, Germany.
| | - Daniel G Pinheiro
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, 14884-900, Jaboticabal, Brazil.
| | - Nina Rossié
- Institute of Evolutionary Genetics, Heinrich Heine University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany.
| | - Olav Rueppell
- Department of Biology, University of North Carolina at Greensboro, 321 McIver Street, Greensboro, NC, 27403, USA.
| | - Carolina G Santos
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, 14040-900, Ribeirão Preto, Brazil.
| | - Regula Schmid-Hempel
- Experimental Ecology, Institute of Integrative Biology, Eidgenössiche Technische Hochschule (ETH) Zürich, CH-8092, Zürich, Switzerland.
| | - Björn D Schmitt
- Institute of Evolutionary Genetics, Heinrich Heine University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany.
| | - Christina Schulte
- Institute of Evolutionary Genetics, Heinrich Heine University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany.
| | - Zilá L P Simões
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, 14040-901, Ribeirão Preto, Brazil.
| | - Michelle P M Soares
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, 14040-900, Ribeirão Preto, Brazil.
| | - Luc Swevers
- Institute of Biosciences & Applications, National Center for Scientific Research Demokritos, Athens, Greece.
| | | | - Florian Wolschin
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA. .,Department of Chemistry, Biotechnology and Food Science, Norwegian University of Food Science, N-1432, Aas, Norway.
| | - Na Yu
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211, Geneva, Switzerland. .,Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211, Geneva, Switzerland.
| | - Peshtewani K Aqrawi
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Kerstin P Blankenburg
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Marcus Coyle
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Liezl Francisco
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Alvaro G Hernandez
- Roy J. Carver Biotechnology Center, University of Illinois Urbana-Champaign, Urbana, IL, USA.
| | - Michael Holder
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Matthew E Hudson
- Department of Crop Sciences and Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - LaRonda Jackson
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Joy Jayaseelan
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Vandita Joshi
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Christie Kovar
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Sandra L Lee
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Robert Mata
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Tittu Mathew
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Irene F Newsham
- Molecular Genetic Technology Program, School of Health Professions, MD Anderson Cancer Center, 1515 Holcombe Blvd, Unit 2, Houston, TX, 77025, USA.
| | - Robin Ngo
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Geoffrey Okwuonu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Christopher Pham
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Ling-Ling Pu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Nehad Saada
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Jireh Santibanez
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - DeNard Simmons
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Rebecca Thornton
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Aarti Venkat
- Department of Human Genetics, University of Chicago, Chicago, IL, USA.
| | - Kimberly K O Walden
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Yuan-Qing Wu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Griet Debyser
- Laboratory of Protein Biochemistry and Biomolecular Engineering, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium.
| | - Bart Devreese
- Laboratory of Protein Biochemistry and Biomolecular Engineering, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium.
| | - Claire Asher
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK.
| | - Julie Blommaert
- Laboratory for Evolution and Development, Genetics Otago and the National Research Centre for Growth and Development, Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand.
| | - Ariel D Chipman
- Department of Ecology, Evolution, and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Lars Chittka
- Department of Biological and Experimental Psychology, School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.
| | - Bertrand Fouks
- Institute of Biology, Martin-Luther-University Halle-Wittenberg, Wittenberg, Germany. .,Department of Biology, University of North Carolina at Greensboro, 321 McIver Street, Greensboro, NC, 27403, USA.
| | - Jisheng Liu
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium. .,School of Life Sciences, Guangzhou University, Guangzhou, China.
| | - Meaghan P O'Neill
- Laboratory for Evolution and Development, Genetics Otago and the National Research Centre for Growth and Development, Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand.
| | - Seirian Sumner
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK.
| | - Daniela Puiu
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA.
| | - Jiaxin Qu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Steven L Salzberg
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA.
| | - Steven E Scherer
- School of Life Sciences, Guangzhou University, Guangzhou, China.
| | - Donna M Muzny
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Gene E Robinson
- Carl R. Woese Institute for Genomic Biology, Department of Entomology, Neuroscience Program, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL, 61801, USA.
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Paul Schmid-Hempel
- Experimental Ecology, Institute of Integrative Biology, Eidgenössiche Technische Hochschule (ETH) Zürich, CH-8092, Zürich, Switzerland.
| | - Kim C Worley
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
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De Oliveira GLV, De Lima KWA, Colombini AM, Pinheiro DG, Panepucci RA, Palma PVB, Brum DG, Covas DT, Simões BP, De Oliveira MC, Donadi EA, Malmegrim KCR. Bone Marrow Mesenchymal Stromal Cells Isolated from Multiple Sclerosis Patients have Distinct Gene Expression Profile and Decreased Suppressive Function Compared with Healthy Counterparts. Cell Transplant 2015; 24:151-65. [DOI: 10.3727/096368913x675142] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Multiple sclerosis (MS) is a chronic inflammatory autoimmune disease of the central nervous system, due to an immune reaction against myelin proteins. Multipotent mesenchymal stromal cells (MSCs) present immunosuppressive effects and have been used for the treatment of autoimmune diseases. In our study, gene expression profile and in vitro immunomodulatory function tests were used to compare bone marrow-derived MSCs obtained from MS patients, at pre- and postautologous hematopoietic stem cell transplantation (AHSCT) with those from healthy donors. Patient MSCs comparatively exhibited i) senescence in culture; ii) similar osteogenic and adipogenic differentiation potential; iii) decreased expression of CD105, CD73, CD44, and HLA-A/B/C molecules; iv) distinct transcription at pre-AHSCT compared with control MSCs, yielding 618 differentially expressed genes, including the downregulation of TGFB1 and HGF genes and modulation of the FGF and HGF signaling pathways; v) reduced antiproliferative effects when pre-AHSCT MSCs were cocultured with allogeneic T-lymphocytes; vi) decreased secretion of IL-10 and TGF-β in supernatants of both cocultures (pre- and post-AHSCT MSCs); and vii) similar percentages of regulatory cells recovered after MSC cocultures. The transcriptional profile of patient MSCs isolated 6 months posttransplantation was closer to pre-AHSCT samples than from healthy MSCs. Considering that patient MSCs exhibited phenotypic changes, distinct transcriptional profile and functional defects implicated in MSC immunomodulatory and immunosuppressive activity, we suggest that further MS clinical studies should be conducted using allogeneic bone marrow MSCs derived from healthy donors. We also demonstrated that treatment of MS patients with AHSCT does not reverse the transcriptional and functional alterations observed in patient MSCs.
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Affiliation(s)
- Gislane L. V. De Oliveira
- Center for Cell-Based Research, Regional Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Kalil W. A. De Lima
- Center for Cell-Based Research, Regional Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Amanda M. Colombini
- Center for Cell-Based Research, Regional Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Daniel G. Pinheiro
- Center for Cell-Based Research, Regional Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Rodrigo A. Panepucci
- Center for Cell-Based Research, Regional Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Patrícia V. B. Palma
- Center for Cell-Based Research, Regional Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Doralina G. Brum
- Department of Neurology, Psychology and Psychiatry, School of Medicine of Botucatu, University of State of São Paulo (UNESP), Botucatu, São Paulo, Brazil
| | - Dimas T. Covas
- Center for Cell-Based Research, Regional Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
- Department of Clinical Medicine, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Belinda P. Simões
- Center for Cell-Based Research, Regional Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
- Department of Clinical Medicine, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Maria C. De Oliveira
- Center for Cell-Based Research, Regional Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
- Department of Clinical Medicine, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Eduardo A. Donadi
- Department of Clinical Medicine, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Kelen C. R. Malmegrim
- Center for Cell-Based Research, Regional Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
- Department of Clinical, Toxicological and Bromatological Analysis, Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
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21
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Mello TRP, Aleixo AC, Pinheiro DG, Nunes FMF, Bitondi MMG, Hartfelder K, Barchuk AR, Simões ZLP. Developmental regulation of ecdysone receptor (EcR) and EcR-controlled gene expression during pharate-adult development of honeybees (Apis mellifera). Front Genet 2014; 5:445. [PMID: 25566327 PMCID: PMC4273664 DOI: 10.3389/fgene.2014.00445] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Accepted: 12/04/2014] [Indexed: 01/04/2023] Open
Abstract
Major developmental transitions in multicellular organisms are driven by steroid hormones. In insects, these, together with juvenile hormone (JH), control development, metamorphosis, reproduction and aging, and are also suggested to play an important role in caste differentiation of social insects. Here, we aimed to determine how EcR transcription and ecdysteroid titers are related during honeybee postembryonic development and what may actually be the role of EcR in caste development of this social insect. In addition, we expected that knocking-down EcR gene expression would give us information on the participation of the respective protein in regulating downstream targets of EcR. We found that in Apis mellifera females, EcR-A is the predominantly expressed variant in postembryonic development, while EcR-B transcript levels are higher in embryos, indicating an early developmental switch in EcR function. During larval and pupal stages, EcR-B expression levels are very low, while EcR-A transcripts are more variable and abundant in workers compared to queens. Strikingly, these transcript levels are opposite to the ecdysteroid titer profile. 20-hydroxyecdysone (20E) application experiments revealed that low 20E levels induce EcR expression during development, whereas high ecdysteroid titers seem to be repressive. By means of RNAi-mediated knockdown (KD) of both EcR transcript variants we detected the differential expression of 234 poly-A+ transcripts encoding genes such as CYPs, MRJPs and certain hormone response genes (Kr-h1 and ftz-f1). EcR-KD also promoted the differential expression of 70 miRNAs, including highly conserved ones (e.g., miR-133 and miR-375), as well honeybee-specific ones (e.g., miR-3745 and miR-3761). Our results put in evidence a broad spectrum of EcR-controlled gene expression during postembryonic development of honeybees, revealing new facets of EcR biology in this social insect.
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Affiliation(s)
- Tathyana R P Mello
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo São Paulo, Brazil
| | - Aline C Aleixo
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo São Paulo, Brazil
| | - Daniel G Pinheiro
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista São Paulo, Brazil
| | - Francis M F Nunes
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos São Carlos, Brazil
| | - Márcia M G Bitondi
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo São Paulo, Brazil
| | - Klaus Hartfelder
- Departamento de Biologia Celular, Molecular e de Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo São Paulo, Brazil
| | - Angel R Barchuk
- Laboratório de Biologia Animal Integrativa, Departamento de Biologia Celular, Tecidual e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas Alfenas, Brazil
| | - Zilá L P Simões
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo São Paulo, Brazil
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22
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Malta TM, Silva IT, Pinheiro DG, Santos AR, Pinto MT, Panepucci RA, Takayanagui OM, Tanaka Y, Covas DT, Kashima S. Altered expression of degranulation-related genes in CD8+ T cells in human T lymphotropic virus type I infection. AIDS Res Hum Retroviruses 2013; 29:826-36. [PMID: 23301858 DOI: 10.1089/aid.2012.0205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Human T lymphotropic virus type I (HTLV-1) is the etiological agent of HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). CD8+ T cells may contribute to the protection or development of HAM/TSP. In this study we used SAGE methodology to screen for differentially expressed genes in CD8+ T cells isolated from HTLV-1 asymptomatic carriers (HAC) and from HAM/TSP patients to identify genes involved in HAM/TSP development. SAGE analysis was conducted by pooling samples according to clinical status. The comparison of gene expression profiles between HAC and HAM/TSP libraries identified 285 differentially expressed tags. We focus on cytotoxicity and cytokine-related genes due to their potential biological role in HTLV-1 infection. Our results showed that patients with HAM/TSP have high expression levels of degranulation-related genes, namely GZMH and PRF1, and of the cytoskeletal adaptor PXN. We found that GZMB and ZAP70 were overexpressed in HTLV-infected patients compared to the noninfected group. We also detected that CCL5 was higher in the HAM/TSP group compared to the HAC and CT groups. Our findings showed that CD8+ T cells of HAM/TSP patients have an inflammatory and active profile. PXN and ZAP70 overexpression in HTLV-1-infected patients was described for the first time here and reinforces this concept. However, although active and abundant, CD8+ T cells are not able to completely eliminate infected cells and prevent the development of HAM/TSP and, moreover, these cells might contribute to the pathogenesis of the disease by migrating to the central nervous system (CNS). These results should be further tested with biological functional assays to increase our understanding on the role of these molecules in the development of HTLV-1-related diseases.
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Affiliation(s)
- Tathiane M. Malta
- National Institute of Science and Technology in Stem Cell and Cell Therapy, Center for Cell Therapy and Regional Blood Center, Blood Center of Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
- Faculty of Pharmaceutical Sciences, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Israel T. Silva
- National Institute of Science and Technology in Stem Cell and Cell Therapy, Center for Cell Therapy and Regional Blood Center, Blood Center of Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
| | - Daniel G. Pinheiro
- National Institute of Science and Technology in Stem Cell and Cell Therapy, Center for Cell Therapy and Regional Blood Center, Blood Center of Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
| | - Anemarie R.D. Santos
- National Institute of Science and Technology in Stem Cell and Cell Therapy, Center for Cell Therapy and Regional Blood Center, Blood Center of Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
| | - Mariana T. Pinto
- National Institute of Science and Technology in Stem Cell and Cell Therapy, Center for Cell Therapy and Regional Blood Center, Blood Center of Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
- Faculty of Pharmaceutical Sciences, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Rodrigo A. Panepucci
- National Institute of Science and Technology in Stem Cell and Cell Therapy, Center for Cell Therapy and Regional Blood Center, Blood Center of Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
- Faculty of Medicine, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | | | - Yuetsu Tanaka
- Department of Immunology, Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Dimas T. Covas
- National Institute of Science and Technology in Stem Cell and Cell Therapy, Center for Cell Therapy and Regional Blood Center, Blood Center of Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
- Faculty of Medicine, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Simone Kashima
- National Institute of Science and Technology in Stem Cell and Cell Therapy, Center for Cell Therapy and Regional Blood Center, Blood Center of Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
- Faculty of Pharmaceutical Sciences, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
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de Lima DS, Martins CS, Paixao BMDC, Amaral FC, Colli LM, Saggioro FP, Neder L, Machado HR, dos Santos ARD, Pinheiro DG, Moreira AC, Silva WA, Castro M. SAGE analysis highlights the putative role of underexpression of ribosomal proteins in GH-secreting pituitary adenomas. Eur J Endocrinol 2012; 167:759-68. [PMID: 22992986 DOI: 10.1530/eje-12-0760] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
BACKGROUND Although the molecular pathogenesis of pituitary adenomas has been assessed by several different techniques, it still remains partially unclear. Ribosomal proteins (RPs) have been recently related to human tumorigenesis, but they have not yet been evaluated in pituitary tumorigenesis. OBJECTIVE The aim of this study was to introduce serial analysis of gene expression (SAGE), a high-throughput method, in pituitary research in order to compare differential gene expression. METHODS Two SAGE cDNA libraries were constructed, one using a pool of mRNA obtained from five GH-secreting pituitary tumors and another from three normal pituitaries. Genes differentially expressed between the libraries were further validated by real-time PCR in 22 GH-secreting pituitary tumors and in 15 normal pituitaries. RESULTS Computer-generated genomic analysis tools identified 13,722 and 14,993 exclusive genes in normal and adenoma libraries respectively. Both shared 6497 genes, 2188 were underexpressed and 4309 overexpressed in tumoral library. In adenoma library, 33 genes encoding RPs were underexpressed. Among these, RPSA, RPS3, RPS14, and RPS29 were validated by real-time PCR. CONCLUSION We report the first SAGE library from normal pituitary tissue and GH-secreting pituitary tumor, which provide quantitative assessment of cellular transcriptome. We also validated some downregulated genes encoding RPs. Altogether, the present data suggest that the underexpression of the studied RP genes possibly collaborates directly or indirectly with other genes to modify cell cycle arrest, DNA repair, and apoptosis, leading to an environment that might have a putative role in the tumorigenesis, introducing new perspectives for further studies on molecular genesis of somatotrophinomas.
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Affiliation(s)
- Deison Soares de Lima
- Department of Internal Medicine, School of Medicine of Ribeirao Preto, University of Sao Paulo, Avenida Bandeirantes 3900, 14049-900 Ribeirao Preto, Sao Paulo, Brazil
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Gordo SMC, Pinheiro DG, Moreira ECO, Rodrigues SM, Poltronieri MC, de Lemos OF, da Silva IT, Ramos RTJ, Silva A, Schneider H, Silva WA, Sampaio I, Darnet S. High-throughput sequencing of black pepper root transcriptome. BMC Plant Biol 2012; 12:168. [PMID: 22984782 PMCID: PMC3487918 DOI: 10.1186/1471-2229-12-168] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Accepted: 08/29/2012] [Indexed: 05/06/2023]
Abstract
BACKGROUND Black pepper (Piper nigrum L.) is one of the most popular spices in the world. It is used in cooking and the preservation of food and even has medicinal properties. Losses in production from disease are a major limitation in the culture of this crop. The major diseases are root rot and foot rot, which are results of root infection by Fusarium solani and Phytophtora capsici, respectively. Understanding the molecular interaction between the pathogens and the host's root region is important for obtaining resistant cultivars by biotechnological breeding. Genetic and molecular data for this species, though, are limited. In this paper, RNA-Seq technology has been employed, for the first time, to describe the root transcriptome of black pepper. RESULTS The root transcriptome of black pepper was sequenced by the NGS SOLiD platform and assembled using the multiple-k method. Blast2Go and orthoMCL methods were used to annotate 10338 unigenes. The 4472 predicted proteins showed about 52% homology with the Arabidopsis proteome. Two root proteomes identified 615 proteins, which seem to define the plant's root pattern. Simple-sequence repeats were identified that may be useful in studies of genetic diversity and may have applications in biotechnology and ecology. CONCLUSIONS This dataset of 10338 unigenes is crucially important for the biotechnological breeding of black pepper and the ecogenomics of the Magnoliids, a major group of basal angiosperms.
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Affiliation(s)
- Sheila MC Gordo
- Genetics and Molecular Biology Laboratory, Coastal Studies Institute, Bragança Campus, Universidade Federal do Pará, Bragança, PA, 68.600-000, Brazil
| | - Daniel G Pinheiro
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Centro Regional de Hemoterapia de Ribeirão Preto, Rua Tenente Catão Roxo, 2501, Ribeirão Preto, SP 14051-140, Brazil
| | - Edith CO Moreira
- Genetics and Molecular Biology Laboratory, Coastal Studies Institute, Bragança Campus, Universidade Federal do Pará, Bragança, PA, 68.600-000, Brazil
| | - Simone M Rodrigues
- EMBRAPA Amazônia Oriental, Trav. Dr. Enéas Pinheiro s/nº, Caixa Postal 48, Belém, PA 66095-100, Brazil
| | - Marli C Poltronieri
- EMBRAPA Amazônia Oriental, Trav. Dr. Enéas Pinheiro s/nº, Caixa Postal 48, Belém, PA 66095-100, Brazil
| | - Oriel F de Lemos
- EMBRAPA Amazônia Oriental, Trav. Dr. Enéas Pinheiro s/nº, Caixa Postal 48, Belém, PA 66095-100, Brazil
| | - Israel Tojal da Silva
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Centro Regional de Hemoterapia de Ribeirão Preto, Rua Tenente Catão Roxo, 2501, Ribeirão Preto, SP 14051-140, Brazil
| | - Rommel TJ Ramos
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Campus Universitário do Guamá, Rua Augusto Corrêa, nº1, Belém, PA 66075-110, Brazil
| | - Artur Silva
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Campus Universitário do Guamá, Rua Augusto Corrêa, nº1, Belém, PA 66075-110, Brazil
| | - Horacio Schneider
- Genetics and Molecular Biology Laboratory, Coastal Studies Institute, Bragança Campus, Universidade Federal do Pará, Bragança, PA, 68.600-000, Brazil
| | - Wilson A Silva
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Centro Regional de Hemoterapia de Ribeirão Preto, Rua Tenente Catão Roxo, 2501, Ribeirão Preto, SP 14051-140, Brazil
| | - Iracilda Sampaio
- Genetics and Molecular Biology Laboratory, Coastal Studies Institute, Bragança Campus, Universidade Federal do Pará, Bragança, PA, 68.600-000, Brazil
| | - Sylvain Darnet
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Campus Universitário do Guamá, Rua Augusto Corrêa, nº1, Belém, PA 66075-110, Brazil
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Silva IT, Pinheiro DG, Silva WA. A computational approach to identify transposable element insertions in cancer cells. Genome Biol 2011. [PMCID: PMC3439072 DOI: 10.1186/gb-2011-12-s1-p28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Silva IT, Pinheiro DG, Silva WA. A computational approach to identify transposable element insertions in cancer cells. Genome Biol 2011. [DOI: 10.1186/1465-6906-12-s1-p28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Galante PAF, Parmigiani RB, Zhao Q, Caballero OL, de Souza JE, Navarro FCP, Gerber AL, Nicolás MF, Salim ACM, Silva APM, Edsall L, Devalle S, Almeida LG, Ye Z, Kuan S, Pinheiro DG, Tojal I, Pedigoni RG, de Sousa RGMA, Oliveira TYK, de Paula MG, Ohno-Machado L, Kirkness EF, Levy S, da Silva WA, Vasconcelos ATR, Ren B, Zago MA, Strausberg RL, Simpson AJG, de Souza SJ, Camargo AA. Distinct patterns of somatic alterations in a lymphoblastoid and a tumor genome derived from the same individual. Nucleic Acids Res 2011; 39:6056-68. [PMID: 21493686 PMCID: PMC3152357 DOI: 10.1093/nar/gkr221] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Although patterns of somatic alterations have been reported for tumor genomes, little is known on how they compare with alterations present in non-tumor genomes. A comparison of the two would be crucial to better characterize the genetic alterations driving tumorigenesis. We sequenced the genomes of a lymphoblastoid (HCC1954BL) and a breast tumor (HCC1954) cell line derived from the same patient and compared the somatic alterations present in both. The lymphoblastoid genome presents a comparable number and similar spectrum of nucleotide substitutions to that found in the tumor genome. However, a significant difference in the ratio of non-synonymous to synonymous substitutions was observed between both genomes (P = 0.031). Protein-protein interaction analysis revealed that mutations in the tumor genome preferentially affect hub-genes (P = 0.0017) and are co-selected to present synergistic functions (P < 0.0001). KEGG analysis showed that in the tumor genome most mutated genes were organized into signaling pathways related to tumorigenesis. No such organization or synergy was observed in the lymphoblastoid genome. Our results indicate that endogenous mutagens and replication errors can generate the overall number of mutations required to drive tumorigenesis and that it is the combination rather than the frequency of mutations that is crucial to complete tumorigenic transformation.
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Affiliation(s)
- Pedro A F Galante
- Ludwig Institute for Cancer Research, São Paulo Branch at Hospital Alemão Oswaldo Cruz, São Paulo 01323-903, Brazil
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Ribeiro-dos-Santos Â, Khayat AS, Silva A, Alencar DO, Lobato J, Luz L, Pinheiro DG, Varuzza L, Assumpção M, Assumpção P, Santos S, Zanette DL, Silva WA, Burbano R, Darnet S. Ultra-deep sequencing reveals the microRNA expression pattern of the human stomach. PLoS One 2010; 5:e13205. [PMID: 20949028 PMCID: PMC2951895 DOI: 10.1371/journal.pone.0013205] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Accepted: 09/08/2010] [Indexed: 02/06/2023] Open
Abstract
Background While microRNAs (miRNAs) play important roles in tissue differentiation and in maintaining basal physiology, little is known about the miRNA expression levels in stomach tissue. Alterations in the miRNA profile can lead to cell deregulation, which can induce neoplasia. Methodology/Principal Findings A small RNA library of stomach tissue was sequenced using high-throughput SOLiD sequencing technology. We obtained 261,274 quality reads with perfect matches to the human miRnome, and 42% of known miRNAs were identified. Digital Gene Expression profiling (DGE) was performed based on read abundance and showed that fifteen miRNAs were highly expressed in gastric tissue. Subsequently, the expression of these miRNAs was validated in 10 healthy individuals by RT-PCR showed a significant correlation of 83.97% (P<0.05). Six miRNAs showed a low variable pattern of expression (miR-29b, miR-29c, miR-19b, miR-31, miR-148a, miR-451) and could be considered part of the expression pattern of the healthy gastric tissue. Conclusions/Significance This study aimed to validate normal miRNA profiles of human gastric tissue to establish a reference profile for healthy individuals. Determining the regulatory processes acting in the stomach will be important in the fight against gastric cancer, which is the second-leading cause of cancer mortality worldwide.
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Rodrigues-Lisoni FC, Peitl P, Vidotto A, Polachini GM, Maniglia JV, Carmona-Raphe J, Cunha BR, Henrique T, Souza CF, Teixeira RAP, Fukuyama EE, Michaluart P, de Carvalho MB, Oliani SM, Tajara EH, Cury PM, de Carvalho MB, Dias-Neto E, Figueiredo DLA, Fukuyama EE, Góis-Filho JF, Leopoldino AM, Mamede RCM, Michaluart-Junior P, Moyses RA, Nóbrega FG, Nóbrega MP, Nunes FD, Ojopi EFB, Serafini LN, Severino P, Silva AMA, Silva WA, Silveira NJF, Souza SCOM, Tajara EH, Wünsch-Filho V, Amar A, Bandeira CM, Braconi MA, Brandão LG, Brandão RM, Canto AL, Cerione M, Cicco R, Chagas MJ, Chedid H, Costa A, Cunha BR, Curioni OA, Fortes CS, Franzi SA, Frizzera APZ, Gazito D, Guimarães PEM, Kaneto CM, López RVM, Macarenco R, Magalhães MR, Meneses C, Mercante AMC, Pinheiro DG, Polachini GM, Rapoport A, Rodini CO, Rodrigues-Lisoni FC, Rodrigues RV, Rossi L, Santos ARD, Santos M, Settani F, Silva FAM, Silva IT, Souza TB, Stabenow E, Takamori JT, Valentim PJ, Vidotto A, Xavier FCA, Yamagushi F, Cominato ML, Correa PMS, Mendes GS, Paiva R, Ramos O, Silva C, Silva MJ, Tarlá MVC. Genomics and proteomics approaches to the study of cancer-stroma interactions. BMC Med Genomics 2010; 3:14. [PMID: 20441585 PMCID: PMC2881110 DOI: 10.1186/1755-8794-3-14] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2009] [Accepted: 05/04/2010] [Indexed: 12/18/2022] Open
Abstract
Background The development and progression of cancer depend on its genetic characteristics as well as on the interactions with its microenvironment. Understanding these interactions may contribute to diagnostic and prognostic evaluations and to the development of new cancer therapies. Aiming to investigate potential mechanisms by which the tumor microenvironment might contribute to a cancer phenotype, we evaluated soluble paracrine factors produced by stromal and neoplastic cells which may influence proliferation and gene and protein expression. Methods The study was carried out on the epithelial cancer cell line (Hep-2) and fibroblasts isolated from a primary oral cancer. We combined a conditioned-medium technique with subtraction hybridization approach, quantitative PCR and proteomics, in order to evaluate gene and protein expression influenced by soluble paracrine factors produced by stromal and neoplastic cells. Results We observed that conditioned medium from fibroblast cultures (FCM) inhibited proliferation and induced apoptosis in Hep-2 cells. In neoplastic cells, 41 genes and 5 proteins exhibited changes in expression levels in response to FCM and, in fibroblasts, 17 genes and 2 proteins showed down-regulation in response to conditioned medium from Hep-2 cells (HCM). Nine genes were selected and the expression results of 6 down-regulated genes (ARID4A, CALR, GNB2L1, RNF10, SQSTM1, USP9X) were validated by real time PCR. Conclusions A significant and common denominator in the results was the potential induction of signaling changes associated with immune or inflammatory response in the absence of a specific protein.
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Pinheiro DG, Galante PAF, de Souza SJ, Zago MA, Silva WA. A score system for quality evaluation of RNA sequence tags: an improvement for gene expression profiling. BMC Bioinformatics 2009; 10:170. [PMID: 19500384 PMCID: PMC2701951 DOI: 10.1186/1471-2105-10-170] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2008] [Accepted: 06/06/2009] [Indexed: 12/01/2022] Open
Abstract
Background High-throughput molecular approaches for gene expression profiling, such as Serial Analysis of Gene Expression (SAGE), Massively Parallel Signature Sequencing (MPSS) or Sequencing-by-Synthesis (SBS) represent powerful techniques that provide global transcription profiles of different cell types through sequencing of short fragments of transcripts, denominated sequence tags. These techniques have improved our understanding about the relationships between these expression profiles and cellular phenotypes. Despite this, more reliable datasets are still necessary. In this work, we present a web-based tool named S3T: Score System for Sequence Tags, to index sequenced tags in accordance with their reliability. This is made through a series of evaluations based on a defined rule set. S3T allows the identification/selection of tags, considered more reliable for further gene expression analysis. Results This methodology was applied to a public SAGE dataset. In order to compare data before and after filtering, a hierarchical clustering analysis was performed in samples from the same type of tissue, in distinct biological conditions, using these two datasets. Our results provide evidences suggesting that it is possible to find more congruous clusters after using S3T scoring system. Conclusion These results substantiate the proposed application to generate more reliable data. This is a significant contribution for determination of global gene expression profiles. The library analysis with S3T is freely available at . S3T source code and datasets can also be downloaded from the aforementioned website.
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Affiliation(s)
- Daniel G Pinheiro
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.
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Chiromatzo AO, Oliveira TYK, Pereira G, Costa AY, Montesco CAE, Gras DE, Yosetake F, Vilar JB, Cervato M, Prado PRR, Cardenas RGCCL, Cerri R, Borges RL, Lemos RN, Alvarenga SM, Perallis VRC, Pinheiro DG, Silva IT, Brandão RM, Cunha MAV, Giuliatti S, Silva WA. miRNApath: a database of miRNAs, target genes and metabolic pathways. Genet Mol Res 2007; 6:859-865. [PMID: 18058708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that regulate target gene expression and hence play important roles in metabolic pathways. Recent studies have evidenced the interrelation of miRNAs with cell proliferation, differentiation, development, and diseases. Since they are involved in gene regulation, they are intrinsically related to metabolic pathways. This leads to questions that are particularly interesting for investigating medical and laboratorial applications. We developed an miRNApath online database that uses miRNA target genes to link miRNAs to metabolic pathways. Currently, databases about miRNA target genes (DIANA miRGen), genomic maps (miRNAMap) and sequences (miRBase) do not provide such correlations. Additionally, miRNApath offers five search services and a download area. For each search, there is a specific type of input, which can be a list of target genes, miRNAs, or metabolic pathways, which results in different views, depending upon the input data, concerning relationships between the target genes, miRNAs and metabolic pathways. There are also internal links that lead to a deeper analysis and cross-links to other databases with more detailed information. miRNApath is being continually updated and is available at http://lgmb.fmrp.usp.br/mirnapath.
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Affiliation(s)
- A O Chiromatzo
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brasil.
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de Souza GA, Godoy LMF, Teixeira VR, Otake AH, Sabino A, Rosa JC, Dinarte AR, Pinheiro DG, Silva WA, Eberlin MN, Chammas R, Greene LJ. Proteomic and SAGE profiling of murine melanoma progression indicates the reduction of proteins responsible for ROS degradation. Proteomics 2006; 6:1460-70. [PMID: 16429458 DOI: 10.1002/pmic.200500243] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Using 2-DE of total cell protein extracts, we compared soluble proteins from murine melanoma lines Tm1 and Tm5 with proteins from the nontumoral cell melan-a from which they were derived. Seventy-one of the 452 spots (average) detected with CBB were differentially accumulated, i.e., increased or decreased twofold. Forty-four spots were identified by PMF/MALDI-TOF, 15 with increased and 29 with decreased protein levels. SAGE showed that 17/34 (50%) of the differentially accumulated proteins, pI range 4-7, presented similar differences at the mRNA level. Major reductions in protein were observed in tumor cells of proteins that degrade reactive oxygen species (ROS). Decreases of > or = twofold in GST, superoxide dismutase, aldehyde dehydrogenase, thioredoxin, peroxiredoxin 2, and peroxiredoxin 6 protein were observed. SAGE indicated the reduction of other proteins involved in ROS degradation. As expected, the accumulation of exogenous peroxides was significantly higher in the tumor cells while the levels of glutathionylation were two times lower in the tumor cells compared to melan-a. The differential accumulation of proteins involved in oncogene/tumor suppressor pathways was observed. Melanoma cells can favor survival pathways activated by ROS by inhibiting p53 pathways and activation of Ras and c-myc pathways.
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Affiliation(s)
- Gustavo A de Souza
- Centro de Terapia Celular, Centro Regional de Hemoterapia de Ribeirão Preto, Centro de Pesquisa, Inovação e Difusão - FAPESP, Brasil
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Ferreira EN, Pires LC, Parmigiani RB, Bettoni F, Puga RD, Pinheiro DG, Andrade LEC, Cruz LO, Degaki TL, Faria M, Festa F, Giannella-Neto D, Giorgi RR, Goldman GH, Granja F, Gruber A, Hackel C, Henrique-Silva F, Malnic B, Manzini CVB, Marie SKN, Martinez-Rossi NM, Oba-Shinjo SM, Pardini MIMC, Rahal P, Rainho CA, Rogatto SR, Romano CM, Rodrigues V, Sales MM, Savoldi M, da Silva IDCG, da Silva NP, de Souza SJ, Tajara EH, Silva WA, Simpson AJG, Sogayar MC, Camargo AA, Carraro DM. Identification and complete sequencing of novel human transcripts through the use of mouse orthologs and testis cDNA sequences. Genet Mol Res 2004; 3:493-511. [PMID: 15688316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
The correct identification of all human genes, and their derived transcripts, has not yet been achieved, and it remains one of the major aims of the worldwide genomics community. Computational programs suggest the existence of 30,000 to 40,000 human genes. However, definitive gene identification can only be achieved by experimental approaches. We used two distinct methodologies, one based on the alignment of mouse orthologous sequences to the human genome, and another based on the construction of a high-quality human testis cDNA library, in an attempt to identify new human transcripts within the human genome sequence. We generated 47 complete human transcript sequences, comprising 27 unannotated and 20 annotated sequences. Eight of these transcripts are variants of previously known genes. These transcripts were characterized according to size, number of exons, and chromosomal localization, and a search for protein domains was undertaken based on their putative open reading frames. In silico expression analysis suggests that some of these transcripts are expressed at low levels and in a restricted set of tissues.
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Affiliation(s)
- Elisa N Ferreira
- Laboratory of Molecular Biology and Genomics, Ludwig Institute for Cancer Research, São Paulo, SP, Brazil
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Sogayar MC, Camargo AA, Bettoni F, Carraro DM, Pires LC, Parmigiani RB, Ferreira EN, de Sá Moreira E, do Rosário D de O Latorre M, Simpson AJG, Cruz LO, Degaki TL, Festa F, Massirer KB, Sogayar MC, Filho FC, Camargo LP, Cunha MAV, De Souza SJ, Faria M, Giuliatti S, Kopp L, de Oliveira PSL, Paiva PB, Pereira AA, Pinheiro DG, Puga RD, S de Souza JE, Albuquerque DM, Andrade LEC, Baia GS, Briones MRS, Cavaleiro-Luna AMS, Cerutti JM, Costa FF, Costanzi-Strauss E, Espreafico EM, Ferrasi AC, Ferro ES, Fortes MAHZ, Furchi JRF, Giannella-Neto D, Goldman GH, Goldman MHS, Gruber A, Guimarães GS, Hackel C, Henrique-Silva F, Kimura ET, Leoni SG, Macedo C, Malnic B, Manzini B CV, Marie SKN, Martinez-Rossi NM, Menossi M, Miracca EC, Nagai MA, Nobrega FG, Nobrega MP, Oba-Shinjo SM, Oliveira MK, Orabona GM, Otsuka AY, Paço-Larson ML, Paixão BMC, Pandolfi JRC, Pardini MIMC, Passos Bueno MR, Passos GAS, Pesquero JB, Pessoa JG, Rahal P, Rainho CA, Reis CP, Ricca TI, Rodrigues V, Rogatto SR, Romano CM, Romeiro JG, Rossi A, Sá RG, Sales MM, Sant'Anna SC, Santarosa PL, Segato F, Silva WA, Silva IDCG, Silva NP, Soares-Costa A, Sonati MF, Strauss BE, Tajara EH, Valentini SR, Villanova FE, Ward LS, Zanette DL. A transcript finishing initiative for closing gaps in the human transcriptome. Genome Res 2004; 14:1413-23. [PMID: 15197164 PMCID: PMC442158 DOI: 10.1101/gr.2111304] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2003] [Accepted: 03/12/2004] [Indexed: 11/24/2022]
Abstract
We report the results of a transcript finishing initiative, undertaken for the purpose of identifying and characterizing novel human transcripts, in which RT-PCR was used to bridge gaps between paired EST clusters, mapped against the genomic sequence. Each pair of EST clusters selected for experimental validation was designated a transcript finishing unit (TFU). A total of 489 TFUs were selected for validation, and an overall efficiency of 43.1% was achieved. We generated a total of 59,975 bp of transcribed sequences organized into 432 exons, contributing to the definition of the structure of 211 human transcripts. The structure of several transcripts reported here was confirmed during the course of this project, through the generation of their corresponding full-length cDNA sequences. Nevertheless, for 21% of the validated TFUs, a full-length cDNA sequence is not yet available in public databases, and the structure of 69.2% of these TFUs was not correctly predicted by computer programs. The TF strategy provides a significant contribution to the definition of the complete catalog of human genes and transcripts, because it appears to be particularly useful for identification of low abundance transcripts expressed in a restricted set of tissues as well as for the delineation of gene boundaries and alternatively spliced isoforms.
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