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Zahid S, Aloe S, Sutherland JH, Holloman WK, Lue NF. Ustilago maydis telomere protein Pot1 harbors an extra N-terminal OB fold and regulates homology-directed DNA repair factors in a dichotomous and context-dependent manner. PLoS Genet 2022; 18:e1010182. [PMID: 35587917 PMCID: PMC9119445 DOI: 10.1371/journal.pgen.1010182] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 04/02/2022] [Indexed: 01/11/2023] Open
Abstract
The telomere G-strand binding protein Pot1 plays multifaceted roles in telomere maintenance and protection. We examined the structure and activities of Pot1 in Ustilago maydis, a fungal model that recapitulates key features of mammalian telomere regulation. Compared to the well-characterized primate and fission yeast Pot1 orthologs, UmPot1 harbors an extra N-terminal OB-fold domain (OB-N), which was recently shown to be present in most metazoans. UmPot1 binds directly to Rad51 and regulates the latter's strand exchange activity. Deleting the OB-N domain, which is implicated in Rad51-binding, caused telomere shortening, suggesting that Pot1-Rad51 interaction facilitates telomere maintenance. Depleting Pot1 through transcriptional repression triggered growth arrest as well as rampant recombination, leading to multiple telomere aberrations. In addition, telomere repeat RNAs transcribed from both the G- and C-strand were dramatically up-regulated, and this was accompanied by elevated levels of telomere RNA-DNA hybrids. Telomere abnormalities of pot1-deficient cells were suppressed, and cell viability was restored by the deletion of genes encoding Rad51 or Brh2 (the BRCA2 ortholog), indicating that homology-directed repair (HDR) proteins are key mediators of telomere aberrations and cellular toxicity. Together, these observations underscore the complex physical and functional interactions between Pot1 and DNA repair factors, leading to context-dependent and dichotomous effects of HDR proteins on telomere maintenance and protection.
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Affiliation(s)
- Syed Zahid
- Department of Microbiology & Immunology, W. R. Hearst Microbiology Research Center, Weill Cornell Medicine, New York, New York, United States of America
| | - Sarah Aloe
- Department of Microbiology & Immunology, W. R. Hearst Microbiology Research Center, Weill Cornell Medicine, New York, New York, United States of America
| | - Jeanette H. Sutherland
- Department of Microbiology & Immunology, W. R. Hearst Microbiology Research Center, Weill Cornell Medicine, New York, New York, United States of America
| | - William K. Holloman
- Department of Microbiology & Immunology, W. R. Hearst Microbiology Research Center, Weill Cornell Medicine, New York, New York, United States of America
| | - Neal F. Lue
- Department of Microbiology & Immunology, W. R. Hearst Microbiology Research Center, Weill Cornell Medicine, New York, New York, United States of America
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, New York, United States of America
- * E-mail:
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Lue NF. Duplex Telomere-Binding Proteins in Fungi With Canonical Telomere Repeats: New Lessons in the Rapid Evolution of Telomere Proteins. Front Genet 2021; 12:638790. [PMID: 33719348 PMCID: PMC7952879 DOI: 10.3389/fgene.2021.638790] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/08/2021] [Indexed: 01/04/2023] Open
Abstract
The telomere protein assemblies in different fungal lineages manifest quite profound structural and functional divergence, implying a high degree of flexibility and adaptability. Previous comparative analyses of fungal telomeres have focused on the role of telomere sequence alterations in promoting the evolution of corresponding proteins, particularly in budding and fission yeast. However, emerging evidence suggests that even in fungi with the canonical 6-bp telomere repeat unit, there are significant remodeling of the telomere assembly. Indeed, a new protein family can be recruited to serve dedicated telomere functions, and then experience subsequent loss in sub-branches of the clade. An especially interesting example is the Tay1 family of proteins, which emerged in fungi prior to the divergence of basidiomycetes from ascomycetes. This relatively recent protein family appears to have acquired its telomere DNA-binding activity through the modification of another Myb-containing protein. Members of the Tay1 family evidently underwent rather dramatic functional diversification, serving, e.g., as transcription factors in fission yeast while acting to promote telomere maintenance in basidiomycetes and some hemi-ascomycetes. Remarkably, despite its distinct structural organization and evolutionary origin, a basidiomycete Tay1 appears to promote telomere replication using the same mechanism as mammalian TRF1, i.e., by recruiting and regulating Blm helicase activity. This apparent example of convergent evolution at the molecular level highlight the ability of telomere proteins to acquire new interaction targets. The remarkable evolutionary history of Tay1 illustrates the power of protein modularity and the facile acquisition of nucleic acid/protein-binding activity to promote telomere flexibility.
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Affiliation(s)
- Neal F Lue
- Department of Microbiology and Immunology, W. R. Hearst Microbiology Research Center, New York, NY, United States.,Sandra and Edward Meyer Cancer Center, Weill Medical College of Cornell University, New York, NY, United States
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Yu EY, Zahid SS, Ganduri S, Sutherland JH, Hsu M, Holloman WK, Lue NF. Structurally distinct telomere-binding proteins in Ustilago maydis execute non-overlapping functions in telomere replication, recombination, and protection. Commun Biol 2020; 3:777. [PMID: 33328546 PMCID: PMC7744550 DOI: 10.1038/s42003-020-01505-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 11/20/2020] [Indexed: 11/09/2022] Open
Abstract
Duplex telomere binding proteins exhibit considerable structural and functional diversity in fungi. Herein we interrogate the activities and functions of two Myb-containing, duplex telomere repeat-binding factors in Ustilago maydis, a basidiomycete that is evolutionarily distant from the standard fungi. These two telomere-binding proteins, UmTay1 and UmTrf2, despite having distinct domain structures, exhibit comparable affinities and sequence specificity for the canonical telomere repeats. UmTay1 specializes in promoting telomere replication and an ALT-like pathway, most likely by modulating the helicase activity of Blm. UmTrf2, in contrast, is critical for telomere protection; transcriptional repression of Umtrf2 leads to severe growth defects and profound telomere aberrations. Comparative analysis of UmTay1 homologs in different phyla reveals broad functional diversity for this protein family and provides a case study for how DNA-binding proteins can acquire and lose functions at various chromosomal locations. Our findings also point to stimulatory effect of telomere protein on ALT in Ustilago maydis that may be conserved in other systems.
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Affiliation(s)
- Eun Young Yu
- Department of Microbiology & Immunology, W. R. Hearst Microbiology Research Center, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Syed S Zahid
- Department of Microbiology & Immunology, W. R. Hearst Microbiology Research Center, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Swapna Ganduri
- Department of Microbiology & Immunology, W. R. Hearst Microbiology Research Center, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Jeanette H Sutherland
- Department of Microbiology & Immunology, W. R. Hearst Microbiology Research Center, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Min Hsu
- Department of Microbiology & Immunology, W. R. Hearst Microbiology Research Center, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - William K Holloman
- Department of Microbiology & Immunology, W. R. Hearst Microbiology Research Center, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Neal F Lue
- Department of Microbiology & Immunology, W. R. Hearst Microbiology Research Center, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA. .,Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA.
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Kwon M, Lee JJ, Min J, Hwang K, Park SG, Kim E, Kim BC, Bhak J, Lee H. Brca2 abrogation engages with the alternative lengthening of telomeres via break‐induced replication. FEBS J 2019; 286:1841-1858. [DOI: 10.1111/febs.14796] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 01/21/2019] [Accepted: 02/25/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Mi‐Sun Kwon
- Department of Biological Sciences Institute of Molecular Biology and Genetics (IMBG) Seoul National University South Korea
| | - Jennifer J. Lee
- Department of Biological Sciences Institute of Molecular Biology and Genetics (IMBG) Seoul National University South Korea
| | - Jaewon Min
- Department of Biological Sciences Institute of Molecular Biology and Genetics (IMBG) Seoul National University South Korea
| | - Kwangwoo Hwang
- Department of Biological Sciences Institute of Molecular Biology and Genetics (IMBG) Seoul National University South Korea
| | - Seung Gu Park
- Department of Biomedical Engineering UNIST Ulsan Korea
| | - Eun‐Hye Kim
- Department of Biomedical Engineering UNIST Ulsan Korea
| | | | - Jong Bhak
- Department of Biomedical Engineering UNIST Ulsan Korea
- Clinomics Inc. Ulsan Korea
| | - Hyunsook Lee
- Department of Biological Sciences Institute of Molecular Biology and Genetics (IMBG) Seoul National University South Korea
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Swapna G, Yu EY, Lue NF. Single telomere length analysis in Ustilago maydis, a high-resolution tool for examining fungal telomere length distribution and C-strand 5'-end processing. MICROBIAL CELL 2018; 5:393-403. [PMID: 30280102 PMCID: PMC6167521 DOI: 10.15698/mic2018.09.645] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Telomeres play important roles in genome stability and cell proliferation. Telomere lengths are heterogeneous and because just a few abnormal telomeres are sufficient to trigger significant cellular response, it is informative to have accurate assays that reveal not only average telomere lengths, but also the distribution of the longest and shortest telomeres in a given sample. Herein we report for the first time, the development of single telomere length analysis (STELA) - a PCR-based assay that amplifies multiple, individual telomeres - for Ustilago maydis, a basidiomycete fungus. Compared to the standard telomere Southern technique, STELA revealed a broader distribution of telomere size as well as the existence of relatively short telomeres in wild type cells. When applied to blm∆, a mutant thought to be defective in telomere replication, STELA revealed preferential loss of long telomeres, whose maintenance may thus be especially dependent upon efficient replication. In comparison to blm∆, the trt1∆ (telomerase null) mutant exhibited greater erosion of short telomeres, consistent with a special role for telomerase in re-lengthening extra-short telomeres. We also used STELA to characterize the 5’ ends of telomere C-strand, and found that in U. maydis, they terminate preferentially at selected nucleotide positions within the telomere repeat. Deleting trt1 altered the 5’-end distributions, suggesting that telomerase may directly or indirectly modulate C-strand 5’ end formation. These findings illustrate the utility of STELA as well as the strengths of U. maydis as a model system for telomere research.
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Affiliation(s)
- Ganduri Swapna
- Department of Microbiology & Immunology, W. R. Hearst Microbiology Research Center, Weill Cornell Medical College, New York, New York, United States of America
| | - Eun Y Yu
- Department of Microbiology & Immunology, W. R. Hearst Microbiology Research Center, Weill Cornell Medical College, New York, New York, United States of America
| | - Neal F Lue
- Department of Microbiology & Immunology, W. R. Hearst Microbiology Research Center, Weill Cornell Medical College, New York, New York, United States of America.,Sandra and Edward Meyer Cancer Center, Weill Cornell Medical College, New York, New York, United States of America
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