Systematic functional profiling of transcription factor networks in Cryptococcus neoformans

Kwang Woo Jung; Dong Hoon Yang; Shinae Maeng; Kyung Tae Lee; Yee Seul So; Joohyeon Hong; Jaeyoung Choi; Hyo Jeong Byun; Hyelim Kim; Soohyun Bang; Min Hee Song; Jang Won Lee; Min Su Kim; Seo Young Kim; Je Hyun Ji; Goun Park; Hyojeong Kwon; Suyeon Cha; Gena Lee Meyers; Li Li Wang; Jooyoung Jang; Guilhem Janbon; Gloria Adedoyin; Taeyup Kim; Anna K. Averette; Joseph Heitman; Eunji Cheong; Yong Hwan Lee; Yin Won Lee; Yong Sun Bahn

doi:10.1038/ncomms7757

Systematic functional profiling of transcription factor networks in Cryptococcus neoformans

Kwang Woo Jung, Dong Hoon Yang, Shinae Maeng, Kyung Tae Lee, Yee Seul So, Joohyeon Hong, Jaeyoung Choi, Hyo Jeong Byun, Hyelim Kim, Soohyun Bang, Min Hee Song, Jang Won Lee, Min Su Kim, Seo Young Kim, Je Hyun Ji, Goun Park, Hyojeong Kwon, Suyeon Cha, Gena Lee Meyers, Li Li WangJooyoung Jang, Guilhem Janbon, Gloria Adedoyin, Taeyup Kim, Anna K. Averette, Joseph Heitman, Eunji Cheong, Yong Hwan Lee, Yin Won Lee, Yong Sun Bahn

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111 Citations (Scopus)

Abstract

Cryptococcus neoformans causes life-threatening meningoencephalitis in humans, but its overall biological and pathogenic regulatory circuits remain elusive, particularly due to the presence of an evolutionarily divergent set of transcription factors (TFs). Here, we report the construction of a high-quality library of 322 signature-tagged gene-deletion strains for 155 putative TF genes previously predicted using the DNA-binding domain TF database, and examine their in vitro and in vivo phenotypic traits under 32 distinct growth conditions. At least one phenotypic trait is exhibited by 145 out of 155 TF mutants (93%) and ∼85% of them (132/155) are functionally characterized for the first time in this study. The genotypic and phenotypic data for each TF are available in the C. neoformans TF phenome database (http://tf.cryptococcus.org). In conclusion, our phenome-based functional analysis of the C. neoformans TF mutant library provides key insights into transcriptional networks of basidiomycetous fungi and human fungal pathogens.

Original language	English
Article number	6757
Journal	Nature communications
Volume	6
DOIs	https://doi.org/10.1038/ncomms7757
Publication status	Published - 2015 Apr 13

Bibliographical note

Funding Information:
We thank Hanna Na, Moonyoung Park, Yongjae Song, Yooyeon Kim, Kyeongseon Ryu, Changho Lee, Ja-Kyung Yoon, Seung-Yeol Lee, Heejung Ahn, Jihwan Lee, Hyunsoo Kim and Sunghyun Kim for their technical assistance in constructing the TF mutant library. This work was supported by National Research Foundation of Korea grants (nos 2008-0061963 and 2010-0029117) from MEST (to Y.-S.B.). This work was also supported in part by NIH/NIAID R01-AI050438-10 to J.H. and ANR (2010-BLAN-1620-01 program YeastIntrons) to G.J.

Publisher Copyright:
© 2015 Macmillan Publishers Limited.

All Science Journal Classification (ASJC) codes

Chemistry(all)
Biochemistry, Genetics and Molecular Biology(all)
General
Physics and Astronomy(all)

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Jung, K. W., Yang, D. H., Maeng, S., Lee, K. T., So, Y. S., Hong, J., Choi, J., Byun, H. J., Kim, H., Bang, S., Song, M. H., Lee, J. W., Kim, M. S., Kim, S. Y., Ji, J. H., Park, G., Kwon, H., Cha, S., Meyers, G. L., ... Bahn, Y. S. (2015). Systematic functional profiling of transcription factor networks in Cryptococcus neoformans. Nature communications, 6, [6757]. https://doi.org/10.1038/ncomms7757

@article{36a5624bcdd64f16ac53ac30d79cdf06,

title = "Systematic functional profiling of transcription factor networks in Cryptococcus neoformans",

abstract = "Cryptococcus neoformans causes life-threatening meningoencephalitis in humans, but its overall biological and pathogenic regulatory circuits remain elusive, particularly due to the presence of an evolutionarily divergent set of transcription factors (TFs). Here, we report the construction of a high-quality library of 322 signature-tagged gene-deletion strains for 155 putative TF genes previously predicted using the DNA-binding domain TF database, and examine their in vitro and in vivo phenotypic traits under 32 distinct growth conditions. At least one phenotypic trait is exhibited by 145 out of 155 TF mutants (93%) and ∼85% of them (132/155) are functionally characterized for the first time in this study. The genotypic and phenotypic data for each TF are available in the C. neoformans TF phenome database (http://tf.cryptococcus.org). In conclusion, our phenome-based functional analysis of the C. neoformans TF mutant library provides key insights into transcriptional networks of basidiomycetous fungi and human fungal pathogens.",

author = "Jung, {Kwang Woo} and Yang, {Dong Hoon} and Shinae Maeng and Lee, {Kyung Tae} and So, {Yee Seul} and Joohyeon Hong and Jaeyoung Choi and Byun, {Hyo Jeong} and Hyelim Kim and Soohyun Bang and Song, {Min Hee} and Lee, {Jang Won} and Kim, {Min Su} and Kim, {Seo Young} and Ji, {Je Hyun} and Goun Park and Hyojeong Kwon and Suyeon Cha and Meyers, {Gena Lee} and Wang, {Li Li} and Jooyoung Jang and Guilhem Janbon and Gloria Adedoyin and Taeyup Kim and Averette, {Anna K.} and Joseph Heitman and Eunji Cheong and Lee, {Yong Hwan} and Lee, {Yin Won} and Bahn, {Yong Sun}",

note = "Funding Information: We thank Hanna Na, Moonyoung Park, Yongjae Song, Yooyeon Kim, Kyeongseon Ryu, Changho Lee, Ja-Kyung Yoon, Seung-Yeol Lee, Heejung Ahn, Jihwan Lee, Hyunsoo Kim and Sunghyun Kim for their technical assistance in constructing the TF mutant library. This work was supported by National Research Foundation of Korea grants (nos 2008-0061963 and 2010-0029117) from MEST (to Y.-S.B.). This work was also supported in part by NIH/NIAID R01-AI050438-10 to J.H. and ANR (2010-BLAN-1620-01 program YeastIntrons) to G.J. Publisher Copyright: {\textcopyright} 2015 Macmillan Publishers Limited.",

year = "2015",

month = apr,

day = "13",

doi = "10.1038/ncomms7757",

language = "English",

volume = "6",

journal = "Nature Communications",

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Jung, KW, Yang, DH, Maeng, S, Lee, KT, So, YS, Hong, J, Choi, J, Byun, HJ, Kim, H, Bang, S, Song, MH, Lee, JW, Kim, MS, Kim, SY, Ji, JH, Park, G, Kwon, H, Cha, S, Meyers, GL, Wang, LL, Jang, J, Janbon, G, Adedoyin, G, Kim, T, Averette, AK, Heitman, J, Cheong, E, Lee, YH, Lee, YW & Bahn, YS 2015, 'Systematic functional profiling of transcription factor networks in Cryptococcus neoformans', Nature communications, vol. 6, 6757. https://doi.org/10.1038/ncomms7757

TY - JOUR

T1 - Systematic functional profiling of transcription factor networks in Cryptococcus neoformans

AU - Jung, Kwang Woo

AU - Yang, Dong Hoon

AU - Maeng, Shinae

AU - Lee, Kyung Tae

AU - So, Yee Seul

AU - Hong, Joohyeon

AU - Choi, Jaeyoung

AU - Byun, Hyo Jeong

AU - Kim, Hyelim

AU - Bang, Soohyun

AU - Song, Min Hee

AU - Lee, Jang Won

AU - Kim, Min Su

AU - Kim, Seo Young

AU - Ji, Je Hyun

AU - Park, Goun

AU - Kwon, Hyojeong

AU - Cha, Suyeon

AU - Meyers, Gena Lee

AU - Wang, Li Li

AU - Jang, Jooyoung

AU - Janbon, Guilhem

AU - Adedoyin, Gloria

AU - Kim, Taeyup

AU - Averette, Anna K.

AU - Heitman, Joseph

AU - Cheong, Eunji

AU - Lee, Yong Hwan

AU - Lee, Yin Won

AU - Bahn, Yong Sun

N1 - Funding Information: We thank Hanna Na, Moonyoung Park, Yongjae Song, Yooyeon Kim, Kyeongseon Ryu, Changho Lee, Ja-Kyung Yoon, Seung-Yeol Lee, Heejung Ahn, Jihwan Lee, Hyunsoo Kim and Sunghyun Kim for their technical assistance in constructing the TF mutant library. This work was supported by National Research Foundation of Korea grants (nos 2008-0061963 and 2010-0029117) from MEST (to Y.-S.B.). This work was also supported in part by NIH/NIAID R01-AI050438-10 to J.H. and ANR (2010-BLAN-1620-01 program YeastIntrons) to G.J. Publisher Copyright: © 2015 Macmillan Publishers Limited.

PY - 2015/4/13

Y1 - 2015/4/13

N2 - Cryptococcus neoformans causes life-threatening meningoencephalitis in humans, but its overall biological and pathogenic regulatory circuits remain elusive, particularly due to the presence of an evolutionarily divergent set of transcription factors (TFs). Here, we report the construction of a high-quality library of 322 signature-tagged gene-deletion strains for 155 putative TF genes previously predicted using the DNA-binding domain TF database, and examine their in vitro and in vivo phenotypic traits under 32 distinct growth conditions. At least one phenotypic trait is exhibited by 145 out of 155 TF mutants (93%) and ∼85% of them (132/155) are functionally characterized for the first time in this study. The genotypic and phenotypic data for each TF are available in the C. neoformans TF phenome database (http://tf.cryptococcus.org). In conclusion, our phenome-based functional analysis of the C. neoformans TF mutant library provides key insights into transcriptional networks of basidiomycetous fungi and human fungal pathogens.

AB - Cryptococcus neoformans causes life-threatening meningoencephalitis in humans, but its overall biological and pathogenic regulatory circuits remain elusive, particularly due to the presence of an evolutionarily divergent set of transcription factors (TFs). Here, we report the construction of a high-quality library of 322 signature-tagged gene-deletion strains for 155 putative TF genes previously predicted using the DNA-binding domain TF database, and examine their in vitro and in vivo phenotypic traits under 32 distinct growth conditions. At least one phenotypic trait is exhibited by 145 out of 155 TF mutants (93%) and ∼85% of them (132/155) are functionally characterized for the first time in this study. The genotypic and phenotypic data for each TF are available in the C. neoformans TF phenome database (http://tf.cryptococcus.org). In conclusion, our phenome-based functional analysis of the C. neoformans TF mutant library provides key insights into transcriptional networks of basidiomycetous fungi and human fungal pathogens.

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Systematic functional profiling of transcription factor networks in Cryptococcus neoformans

Abstract

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