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Hazan JM, Amador R, Ali-Nasser T, Lahav T, Shotan SR, Steinberg M, Cohen Z, Aran D, Meiri D, Assaraf YG, Guigó R, Bester AC. Integration of transcription regulation and functional genomic data reveals lncRNA SNHG6's role in hematopoietic differentiation and leukemia. J Biomed Sci 2024; 31:27. [PMID: 38419051 PMCID: PMC10900714 DOI: 10.1186/s12929-024-01015-8] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 02/22/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) are pivotal players in cellular processes, and their unique cell-type specific expression patterns render them attractive biomarkers and therapeutic targets. Yet, the functional roles of most lncRNAs remain enigmatic. To address the need to identify new druggable lncRNAs, we developed a comprehensive approach integrating transcription factor binding data with other genetic features to generate a machine learning model, which we have called INFLAMeR (Identifying Novel Functional LncRNAs with Advanced Machine Learning Resources). METHODS INFLAMeR was trained on high-throughput CRISPR interference (CRISPRi) screens across seven cell lines, and the algorithm was based on 71 genetic features. To validate the predictions, we selected candidate lncRNAs in the human K562 leukemia cell line and determined the impact of their knockdown (KD) on cell proliferation and chemotherapeutic drug response. We further performed transcriptomic analysis for candidate genes. Based on these findings, we assessed the lncRNA small nucleolar RNA host gene 6 (SNHG6) for its role in myeloid differentiation. Finally, we established a mouse K562 leukemia xenograft model to determine whether SNHG6 KD attenuates tumor growth in vivo. RESULTS The INFLAMeR model successfully reconstituted CRISPRi screening data and predicted functional lncRNAs that were previously overlooked. Intensive cell-based and transcriptomic validation of nearly fifty genes in K562 revealed cell type-specific functionality for 85% of the predicted lncRNAs. In this respect, our cell-based and transcriptomic analyses predicted a role for SNHG6 in hematopoiesis and leukemia. Consistent with its predicted role in hematopoietic differentiation, SNHG6 transcription is regulated by hematopoiesis-associated transcription factors. SNHG6 KD reduced the proliferation of leukemia cells and sensitized them to differentiation. Treatment of K562 leukemic cells with hemin and PMA, respectively, demonstrated that SNHG6 inhibits red blood cell differentiation but strongly promotes megakaryocyte differentiation. Using a xenograft mouse model, we demonstrate that SNHG6 KD attenuated tumor growth in vivo. CONCLUSIONS Our approach not only improved the identification and characterization of functional lncRNAs through genomic approaches in a cell type-specific manner, but also identified new lncRNAs with roles in hematopoiesis and leukemia. Such approaches can be readily applied to identify novel targets for precision medicine.
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Affiliation(s)
- Joshua M Hazan
- Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
| | - Raziel Amador
- Centre for Genomic Regulation (CRG), Doctor Aiguader 88, 08003, Barcelona, Catalonia, Spain
- Universitat de Barcelona (UB), Barcelona, Catalonia, Spain
| | - Tahleel Ali-Nasser
- Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
| | - Tamar Lahav
- Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
| | - Stav Roni Shotan
- Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
| | - Miryam Steinberg
- Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
| | - Ziv Cohen
- Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
- The Taub Faculty of Computer Science, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
| | - Dvir Aran
- Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
- The Taub Faculty of Computer Science, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
| | - David Meiri
- Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
| | - Yehuda G Assaraf
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), Doctor Aiguader 88, 08003, Barcelona, Catalonia, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain
| | - Assaf C Bester
- Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel.
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Alfi O, Cohen M, Bar-On S, Hashimshony T, Levitt L, Raz Y, Blecher Y, Chaudhry MZ, Cicin-Sain L, Ben-El R, Oiknine-Djian E, Lahav T, Vorontsov O, Cohen A, Zakay-Rones Z, Daniel L, Berger M, Mandel-Gutfreund Y, Panet A, Wolf DG. Decidual-tissue-resident memory T cells protect against nonprimary human cytomegalovirus infection at the maternal-fetal interface. Cell Rep 2024; 43:113698. [PMID: 38265934 DOI: 10.1016/j.celrep.2024.113698] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 11/14/2023] [Accepted: 01/05/2024] [Indexed: 01/26/2024] Open
Abstract
Congenital cytomegalovirus (cCMV) is the most common intrauterine infection, leading to infant neurodevelopmental disabilities. An improved knowledge of correlates of protection against cCMV is needed to guide prevention strategies. Here, we employ an ex vivo model of human CMV (HCMV) infection in decidual tissues of women with and without preconception immunity against CMV, recapitulating nonprimary vs. primary infection at the authentic maternofetal transmission site. We show that decidual tissues of women with preconception immunity against CMV exhibit intrinsic resistance to HCMV, mounting a rapid activation of tissue-resident memory CD8+ and CD4+ T cells upon HCMV reinfection. We further reveal the role of HCMV-specific decidual-tissue-resident CD8+ T cells in local protection against nonprimary HCMV infection. The findings could inform the development of a vaccine against cCMV and provide insights for further studies of the integrity of immune defense against HCMV and other pathogens at the human maternal-fetal interface.
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Affiliation(s)
- Or Alfi
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem, Israel; Department of Biochemistry, Institute for Medical Research Israel Canada, Faculty of Medicine, The Hebrew University, Jerusalem, Israel; Lautenberg Center for General and Tumor Immunology, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Mevaseret Cohen
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem, Israel; Department of Biochemistry, Institute for Medical Research Israel Canada, Faculty of Medicine, The Hebrew University, Jerusalem, Israel; Lautenberg Center for General and Tumor Immunology, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Shikma Bar-On
- Lis Maternity Hospital, Tel Aviv Souraski Medical Center, Tel Aviv, Israel; Affiliated with the Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Tamar Hashimshony
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Lorinne Levitt
- Department of Obstetrics and Gynecology, Hadassah Hebrew University Medical Center and Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yael Raz
- Lis Maternity Hospital, Tel Aviv Souraski Medical Center, Tel Aviv, Israel; Affiliated with the Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yair Blecher
- Lis Maternity Hospital, Tel Aviv Souraski Medical Center, Tel Aviv, Israel; Affiliated with the Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - M Zeeshan Chaudhry
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany; German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany
| | - Luka Cicin-Sain
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany; German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany; Centre for Individualised Infection Medicine (a joint venture of HZI and MHH), Hannover, Germany
| | - Rina Ben-El
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Esther Oiknine-Djian
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem, Israel; Lautenberg Center for General and Tumor Immunology, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Tamar Lahav
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Olesya Vorontsov
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem, Israel; Department of Biochemistry, Institute for Medical Research Israel Canada, Faculty of Medicine, The Hebrew University, Jerusalem, Israel; Lautenberg Center for General and Tumor Immunology, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Adiel Cohen
- Department of Obstetrics and Gynecology, Hadassah Hebrew University Medical Center and Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Zichria Zakay-Rones
- Department of Biochemistry, Institute for Medical Research Israel Canada, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Leonor Daniel
- Lautenberg Center for General and Tumor Immunology, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Michael Berger
- Lautenberg Center for General and Tumor Immunology, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | | | - Amos Panet
- Department of Biochemistry, Institute for Medical Research Israel Canada, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Dana G Wolf
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem, Israel; Lautenberg Center for General and Tumor Immunology, Faculty of Medicine, The Hebrew University, Jerusalem, Israel.
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Gilda JE, Nahar A, Kasiviswanathan D, Tropp N, Gilinski T, Lahav T, Mandel-Gutfreund Y, Park S, Cohen S. Proteasome gene expression is controlled by the coordinated functions of multiple transcription factors. bioRxiv 2023:2023.04.12.536627. [PMID: 37205440 PMCID: PMC10187252 DOI: 10.1101/2023.04.12.536627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Proteasome activity is crucial for cellular integrity, but how tissues adjust proteasome content in response to catabolic stimuli is uncertain. Here, we demonstrate that transcriptional coordination by multiple transcription factors is required to increase proteasome content and activate proteolysis in catabolic states. Using denervated mouse muscle as a model system for accelerated proteolysis in vivo , we reveal that a two-phase transcriptional program activates genes encoding proteasome subunits and assembly chaperones to boost an increase in proteasome content. Initially, gene induction is necessary to maintain basal proteasome levels, and in a more delayed phase (7-10 d after denervation) it stimulates proteasome assembly to meet cellular demand for excessive proteolysis. Intriguingly, the transcription factors PAX4 and α-PAL NRF-1 control the expression of proteasome among other genes in a combinatorial manner, driving cellular adaptation to muscle denervation. Consequently, PAX4 and α-PAL NRF-1 represent new therapeutic targets to inhibit proteolysis in catabolic diseases (e.g. type-2 diabetes, cancer).
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Opatovsky I, Santos-Garcia D, Ruan Z, Lahav T, Ofaim S, Mouton L, Barbe V, Jiang J, Zchori-Fein E, Freilich S. Modeling trophic dependencies and exchanges among insects' bacterial symbionts in a host-simulated environment. BMC Genomics 2018; 19:402. [PMID: 29801436 PMCID: PMC5970531 DOI: 10.1186/s12864-018-4786-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [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: 09/14/2017] [Accepted: 05/11/2018] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Individual organisms are linked to their communities and ecosystems via metabolic activities. Metabolic exchanges and co-dependencies have long been suggested to have a pivotal role in determining community structure. In phloem-feeding insects such metabolic interactions with bacteria enable complementation of their deprived nutrition. The phloem-feeding whitefly Bemisia tabaci (Hemiptera: Aleyrodidae) harbors an obligatory symbiotic bacterium, as well as varying combinations of facultative symbionts. This well-defined bacterial community in B. tabaci serves here as a case study for a comprehensive and systematic survey of metabolic interactions within the bacterial community and their associations with documented occurrences of bacterial combinations. We first reconstructed the metabolic networks of five common B. tabaci symbionts genera (Portiera, Rickettsia, Hamiltonella, Cardinium and Wolbachia), and then used network analysis approaches to predict: (1) species-specific metabolic capacities in a simulated bacteriocyte-like environment; (2) metabolic capacities of the corresponding species' combinations, and (3) dependencies of each species on different media components. RESULTS The predictions for metabolic capacities of the symbionts in the host environment were in general agreement with previously reported genome analyses, each focused on the single-species level. The analysis suggests several previously un-reported routes for complementary interactions and estimated the dependency of each symbiont in specific host metabolites. No clear association was detected between metabolic co-dependencies and co-occurrence patterns. CONCLUSIONS The analysis generated predictions for testable hypotheses of metabolic exchanges and co-dependencies in bacterial communities and by crossing them with co-occurrence profiles, contextualized interaction patterns into a wider ecological perspective.
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Affiliation(s)
- Itai Opatovsky
- Newe Ya’ar Research Center, The Agricultural Research Organization, Ramat Yishay, Israel
- Agricultural Research and Development Center, Southern Branch (Besor), Israel
| | | | - Zhepu Ruan
- Newe Ya’ar Research Center, The Agricultural Research Organization, Ramat Yishay, Israel
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095 China
| | - Tamar Lahav
- Newe Ya’ar Research Center, The Agricultural Research Organization, Ramat Yishay, Israel
| | - Shany Ofaim
- Newe Ya’ar Research Center, The Agricultural Research Organization, Ramat Yishay, Israel
| | - Laurence Mouton
- CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR CNRS 5558, Université de Lyon, Université Claude Bernard, F-69622 Villeurbanne, France
| | - Valérie Barbe
- Institut de biologie François-Jacob, GenoscopeCEA, Genoscope, Evry, France
| | - Jiandong Jiang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095 China
| | - Einat Zchori-Fein
- Newe Ya’ar Research Center, The Agricultural Research Organization, Ramat Yishay, Israel
| | - Shiri Freilich
- Newe Ya’ar Research Center, The Agricultural Research Organization, Ramat Yishay, Israel
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5
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Iasur Kruh L, Lahav T, Abu-Nassar J, Achdari G, Salami R, Freilich S, Aly R. Host-Parasite-Bacteria Triangle: The Microbiome of the Parasitic Weed Phelipanche aegyptiaca and Tomato- Solanum lycopersicum (Mill.) as a Host. Front Plant Sci 2017; 8:269. [PMID: 28298918 PMCID: PMC5331046 DOI: 10.3389/fpls.2017.00269] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 02/14/2017] [Indexed: 05/28/2023]
Abstract
Broomrapes (Phelipanche/Orobanche spp.) are holoparasitic plants that subsist on the roots of a variety of agricultural crops, establishing direct connections with the host vascular system. This connection allows for the exchange of various substances and a possible exchange of endophytic microorganisms that inhabit the internal tissues of both plants. To shed some light on bacterial interactions occurring between the parasitic Phelipanche aegyptiaca and its host tomato, we characterized the endophytic composition in the parasite during the parasitization process and ascertained if these changes were accompanied by changes to endophytes in the host root. Endophyte communities of the parasitic weed were significantly different from that of the non-parasitized tomato root but no significant differences were observed between the parasite and its host after parasitization, suggesting the occurrence of bacterial exchange between these two plants. Moreover, the P. aegyptiaca endophytic community composition showed a clear shift from gram negative to gram-positive bacteria at different developmental stages of the parasite life cycle. To examine possible functions of the endophytic bacteria in both the host and the parasite plants, a number of unique bacterial candidates were isolated and characterized. Results showed that a Pseudomonas strain PhelS10, originating from the tomato roots, suppressed approximately 80% of P. aegyptiaca seed germination and significantly reduced P. aegyptiaca parasitism. The information gleaned in the present study regarding the endophytic microbial communities in this unique ecological system of two plants connected by their vascular system, highlights the potential of exploiting alternative environmentally friendly approaches for parasitic weed control.
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Affiliation(s)
- Lilach Iasur Kruh
- Department of Weed Science, Newe Ya’ar Research Center, Agricultural Research OrganizationRamat Yishay, Israel
- Department of Biotechnology Engineering, ORT Braude CollegeKarmiel, Israel
| | - Tamar Lahav
- The Institute of Plant Sciences, Newe Ya’ar Research Center, Agricultural Research OrganizationRamat Yishay, Israel
| | - Jacline Abu-Nassar
- Department of Weed Science, Newe Ya’ar Research Center, Agricultural Research OrganizationRamat Yishay, Israel
| | - Guy Achdari
- Department of Weed Science, Newe Ya’ar Research Center, Agricultural Research OrganizationRamat Yishay, Israel
| | - Raghda Salami
- Department of Biotechnology Engineering, ORT Braude CollegeKarmiel, Israel
| | - Shiri Freilich
- The Institute of Plant Sciences, Newe Ya’ar Research Center, Agricultural Research OrganizationRamat Yishay, Israel
| | - Radi Aly
- Department of Weed Science, Newe Ya’ar Research Center, Agricultural Research OrganizationRamat Yishay, Israel
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Yadav BS, Lahav T, Reuveni E, Chamovitz DA, Freilich S. Multidimensional patterns of metabolic response in abiotic stress-induced growth of Arabidopsis thaliana. Plant Mol Biol 2016; 92:689-699. [PMID: 27633976 DOI: 10.1007/s11103-016-0539-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Accepted: 08/29/2016] [Indexed: 05/11/2023]
Abstract
Contextualization of specific transcriptional responses of Arabidopsis within the stress-tissue-time perspective provides a simplified representation of the cellular transcriptional response pathways to abiotic stress, while reducing the dimensions in gene-oriented response description. Crops resistant to abiotic stresses are a long-term goal of many research programs, thus understanding the progression of stress responses is of great interest. We reanalyzed the AtGenExpress transcription dataset to go beyond gene-level characterization, and to contextualize the discrete information into (1) a process-level signature of stress-specific, time-specific, and tissue-specific responses and (2) identify patterns of response progression across a time axis. To gain a functional perspective, ∼1000 pathways associated with the differentially-expressed genes were characterized across all experiments. We find that the global response of pathways to stress is multi-dimensional and does not obviously cluster according to stress, time or tissue. The early response to abiotic stress typically involves induction of genes involved in transcription, hormone synthesis and signaling modules; a later response typically involves metabolism of amino acids and secondary metabolites. By linking specific primary and secondary response pathways, we outline possible stress-associated routes of response progression. The contextualization of specific processes within stress-tissue-time perspective provides a simplified representation of cellular response while reducing the dimensions in gene-oriented response description. Such simplified representation allows finding stress-specific markers based on process-combinations pointing whether a stress-specific response was invoked as well as provide a reference point for the conductance of comparative inter-plant study of stress response, bypassing the need in detailed orthologous mapping.
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Affiliation(s)
- Brijesh S Yadav
- Department of Molecular Biology and Ecology of Plants, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Tamar Lahav
- Newe-Ya'ar Research Center, Institute of Plant Sciences, Agricultural Research Organization, PO Box 1021, 30095, Ramat Yishay, Israel
| | - Eli Reuveni
- Newe-Ya'ar Research Center, Institute of Plant Sciences, Agricultural Research Organization, PO Box 1021, 30095, Ramat Yishay, Israel
| | - Daniel A Chamovitz
- Department of Molecular Biology and Ecology of Plants, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
| | - Shiri Freilich
- Newe-Ya'ar Research Center, Institute of Plant Sciences, Agricultural Research Organization, PO Box 1021, 30095, Ramat Yishay, Israel.
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Zchori-Fein E, Lahav T, Freilich S. Variations in the identity and complexity of endosymbiont combinations in whitefly hosts. Front Microbiol 2014; 5:310. [PMID: 25071729 PMCID: PMC4092360 DOI: 10.3389/fmicb.2014.00310] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [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: 03/31/2014] [Accepted: 06/06/2014] [Indexed: 11/22/2022] Open
Abstract
The target of natural selection is suggested to be the holobiont - the organism together with its associated symbiotic microorganisms. The well-defined endosymbiotic communities of insects make them a useful model for exploring the role of symbiotic interactions in shaping the functional repertoire of plants and animals. Here, we studied the variations in the symbiotic communities of the sweet potato whitefly Bemisia tabaci (Hemiptera: Aleyrodidae) by compiling a dataset of over 2000 individuals derived from several independent screenings. The secondary endosymbionts harbored by each individual were clustered into entities termed Facultative Endosymbiont Combinations (FECs), each representing a natural assemblage of co-occurring bacterial genera. The association of FECs with whitefly individuals stratified the otherwise homogeneous population into holobiont units. We both identified bacterial assemblages that are specific to whitefly groups sharing unique genetic backgrounds, and characterized the FEC variations within these groups. The analysis revealed that FEC complexity is positively correlated with both distance from the equator and specificity of the genetic clade of the host insect. These findings highlight the importance of symbiotic combinations in shaping the distribution patterns of B. tabaci and possibly other insect species.
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Affiliation(s)
- Einat Zchori-Fein
- The Agricultural Research Organization, Newe Ya'ar Research Center, Institute of Plant Protection Ramat Yishay, Israel
| | - Tamar Lahav
- The Agricultural Research Organization, Newe Ya'ar Research Center, Institute of Plant Sciences Ramat Yishay, Israel
| | - Shiri Freilich
- The Agricultural Research Organization, Newe Ya'ar Research Center, Institute of Plant Sciences Ramat Yishay, Israel
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Lahav T, Sivam D, Volpin H, Ronen M, Tsigankov P, Green A, Holland N, Kuzyk M, Borchers C, Zilberstein D, Myler PJ. Multiple levels of gene regulation mediate differentiation of the intracellular pathogen Leishmania. FASEB J 2010; 25:515-25. [PMID: 20952481 DOI: 10.1096/fj.10-157529] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
For many years, mRNA abundance has been used as the surrogate measure of gene expression in biological systems. However, recent genome-scale analyses in both bacteria and eukaryotes have revealed that mRNA levels correlate with steady-state protein abundance for only 50-70% of genes, indicating that translation and post-translation processes also play important roles in determining gene expression. What is not yet clear is whether dynamic processes such as cell cycle progression, differentiation, or response to environmental changes change the relationship between mRNA and protein abundance. Here, we describe a systems approach to interrogate promastigote-to-amastigote differentiation in the obligatory intracellular parasitic protozoan Leishmania donovani. Our results indicate that regulation of mRNA levels plays a major role early in the differentiation process, while translation and post-translational regulation are more important in the latter part. In addition, it appears that the differentiation signal causes a transient global increase in the rate of protein synthesis, which is subsequently down-regulated by phosphorylation of α-subunit of translation initiation factor 2. Thus, Leishmania dynamically changes the relationship between mRNA and protein abundance as it adapts to new environmental circumstances. It is likely that similar mechanisms play a more important role than previously recognized in regulation of gene expression in other organisms.
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Affiliation(s)
- T Lahav
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
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9
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Saxena A, Lahav T, Holland N, Aggarwal G, Anupama A, Huang Y, Volpin H, Myler PJ, Zilberstein D. Analysis of the Leishmania donovani transcriptome reveals an ordered progression of transient and permanent changes in gene expression during differentiation. Mol Biochem Parasitol 2006; 152:53-65. [PMID: 17204342 PMCID: PMC1904838 DOI: 10.1016/j.molbiopara.2006.11.011] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2006] [Revised: 11/18/2006] [Accepted: 11/22/2006] [Indexed: 01/22/2023]
Abstract
Leishmania donovani is an intracellular protozoan parasite that causes kala-azar in humans. During infection the extracellular insect forms (promastigotes) undergo rapid differentiation to intracellular amastigotes that proliferates in phagolysosomes of mammalian macrophages. We used microarray-based expression profiling to investigate the time-course of changes in RNA abundance during promastigote-to-amastigote differentiation in a host-free system that mimics this process. These studies revealed that several hundred genes underwent an ordered progression of transient or permanent up- and down-regulation during differentiation. Genes that were permanently up-regulated in amastigotes were enriched for transporters and surface proteins, but under-represented in genes involved in protein and other metabolism. Most of these changes occurred late in the differentiation process, when morphological differentiation was essentially complete. Down-regulated genes were over-represented in those involved in cell motility, growth and/or maintenance, and these changes generally occurred earlier in the process. Genes that were transiently up- or down-regulated during differentiation included those encoding heat shock proteins, ubiquitin hydrolases, RNA binding proteins, protein kinases, a protein phosphatase, and a histone deacetylase. These results suggest that changes in mRNA abundance may be important in signal transduction, as well as protein and mRNA turnover, during differentiation. In addition to these mRNA changes, other transcripts including one or more rRNAs and snoRNAs, and non-coding RNAs from several telomeres, also showed substantial changes in abundance during the differentiation process. This paper provides the first genome-scale quantitative analysis of gene expression during the transition from promastigotes to amastigotes and demonstrates the utility of the host-free differentiation system.
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Affiliation(s)
- A Saxena
- Seattle Biomedical Research Institute, 307 Westlake Avenue N, Seattle, WA 98109-5219, USA
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Lahav T, Atzmon G, Blum S, Ben-Ari G, Weigend S, Cahaner A, Lavi U, Hillel J. Marker-assisted selection based on a multi-trait economic index in chicken: experimental results and simulation. Anim Genet 2006; 37:482-8. [PMID: 16978178 DOI: 10.1111/j.1365-2052.2006.01512.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [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: 11/28/2022]
Abstract
A method proposed herein allows simultaneous selection for several production traits, taking into consideration their marginal economic values (i.e. the economic value of a trait's additional unit). This economic index-marker assisted selection (EI-MAS) method is based on the calculation of the predicted economic breeding value (BV), using information on DNA markers that have previously been found to be associated with relevant quantitative trait loci. Based on the proposed method, results with real birds showed that sire progeny performance was significantly correlated with expected performance (r = 0.61-0.76; P = 0.03-0.01). Simulation analysis using a computer program written specifically for this purpose suggested that the relative advantage of EI-MAS would be large for traits with low heritability values. As expected, the response to EI-MAS was higher when the map distance between the marker and the quantitative trait gene was small, and vice versa. A large number of distantly located markers, spread 10 cM apart, yielded higher response to selection than a small number of closely located markers spread 3 cM apart. Additionally, the response to EI-MAS was higher when a large number (ca.150) of progeny was used for the prediction equation.
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Affiliation(s)
- T Lahav
- The Robert H. Smith Institute of Plant Sciences & Genetics, The Hebrew University of Jerusalem, Rehovot 76100, Israel
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Abstract
The performance of a novel, rapid, and sensitive test for detecting chemical toxicants in water is described in this article. The bioassay utilizes a highly sensitive variant of the luminescent bacterium Photobacterium leiognathi that allows the detection in water at levels below milligrams per liter of diverse groups of toxicants, including heavy metals, pesticides, PCBs, polycyclic aromatic hydrocarbons, and fuel traces. For most toxic agents reported in this study, the new assay was markedly more sensitive than the Microtox(trade mark) Vibrio fischeri assay according to the bacterial bioluminescence toxicity data reported in the literature. Additional features of the new bioassay include the ability to discriminate between cationic heavy metals and organic toxicants and the option of being run at ambient temperatures (18 degrees C-27 degrees C), thereby enabling on-site testing with low-cost luminometers. In addition, the stability of the freeze-dried bacterial reagent preparation at ambient temperatures precludes the need for refrigeration or freezing during shipment, which contributes to further reducing overall operational costs.
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Affiliation(s)
- S Ulitzur
- Department of Food Engineering and Biotechnology, Technion Institute, Haifa 32000, Israel.
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