The PAC-3 transcription factor critically regulates phenotype-associated genes in <i>Neurospora crassa</i>

Martins, Maíra Pompeu; Martinez-Rossi, Nilce Maria; Sanches, Pablo Rodrigo; Rossi, Antonio

doi:10.1590/1678-4685-GMB-2019-0374

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Sumário

Genetics of Microorganisms • Genet. Mol. Biol. 43 (3) • 2020 • https://doi.org/10.1590/1678-4685-GMB-2019-0374 copy

The PAC-3 transcription factor critically regulates phenotype-associated genes in Neurospora crassa

Authorship SCIMAGO INSTITUTIONS RANKINGS

Abstract

Transcription factors play an important role in fungal environmental adaptive process by promoting adjustment to challenging stimuli via gene modulation and activation of signaling networks. The transcription factor encoded by the pac-3/rim101/pacC gene is involved in pH regulation and is associated with a wide variety of cellular functions. The deletion of pac-3 affects fungal development. In Neurospora crassa, the Δpac-3 strain presents diminished aerial growth and reduced conidiation. However, the PAC-3-regulated genes associated with this altered phenotype have not been elucidated. In this study, we used RNA-seq to analyze the phenotypic plasticity induced after pac-3 deletion in the filamentous fungus N. crassa cultivated in media supplemented with sufficient or limited inorganic phosphate. Genes related to morphology, hyphal development, and conidiation were of particular interest in this study. Our results suggest a pac-3 dependency in gene regulation in a Pi-dependent manner. Furthermore, our analysis suggested that the fungus attempts to overcome the deletion effects in a Δpac-3 mutant through a complex combined regulatory mechanism. Finally, the modulatory responses observed in the Δpac-3 strain, a double mutant generated based on the Δmus-52 mutant strain, is strain-specific, highlighting that the phenotypic impact may be attributed to pac-3 absence despite the combined mus-52 deletion.

Keywords:
RNA-seq; conidiation; hyphal development; transcription factor; inorganic phosphate

GO ID	Gene ID	Gene Product Name	Δpac-3 vs. Δmus-52		Δmus-52 vs. 74A
			low-Pi	high-Pi	low-Pi	high-Pi
GO:0006355	NCU04058^‡ ‡ Genes presenting binding motif for PAC-3 in their promoter region. ^† † Transcription factors	BZIP domain-containing protein		3.00	2.77
GO:0043666	NCU01504^‡ ‡ Genes presenting binding motif for PAC-3 in their promoter region.	Calcineurin binding protein		2.15
GO:0070884
GO:0006357	NCU08852^‡ ‡ Genes presenting binding motif for PAC-3 in their promoter region.	Poly(ADP-ribose) polymerase		2.18	2.66
GO:0030435	NCU08726^‡ ‡ Genes presenting binding motif for PAC-3 in their promoter region. ^† † Transcription factors	Fluffy		1.94
GO:0048315
GO:0006357
GO:0006355	NCU03650^‡ ‡ Genes presenting binding motif for PAC-3 in their promoter region.	DNA repair protein RAD16		1.55	1.77
Unannotated	NCU04197^‡ ‡ Genes presenting binding motif for PAC-3 in their promoter region.	CipC protein	6.62	8.44
GO:0006357	NCU00282^‡ ‡ Genes presenting binding motif for PAC-3 in their promoter region. ^† † Transcription factors	Zn(2)-C6 fungal-type domain-containing protein	3.89	4.34
GO:0046830	NCU07723^‡ ‡ Genes presenting binding motif for PAC-3 in their promoter region.	Norsolorinic acid reductase	3.08	2.26
GO:0006357	NCU04866^‡ ‡ Genes presenting binding motif for PAC-3 in their promoter region. ^† † Transcription factors	All development altered-6	2.00	2.15
GO:0033499	NCU04442^‡ ‡ Genes presenting binding motif for PAC-3 in their promoter region.	GAL10	1.73	1.77
GO:0000122	NCU08055^‡ ‡ Genes presenting binding motif for PAC-3 in their promoter region. ^† † Transcription factors	B-ZIP transcription factor IDI4	1.60	2.45
GO:0001080
GO:0045944
GO:1903833
GO:0007165	NCU06111^‡ ‡ Genes presenting binding motif for PAC-3 in their promoter region.	GTPase Ras2p	1.55	1.52
Unannotated	NCU09629^‡ ‡ Genes presenting binding motif for PAC-3 in their promoter region.	Hypothetical protein	-1.81	2.12		-3.14
Unannotated	NCU04605^‡ ‡ Genes presenting binding motif for PAC-3 in their promoter region.	Hypothetical protein	-2.61			-3.39
GO:0043934	NCU00586^‡ ‡ Genes presenting binding motif for PAC-3 in their promoter region.	Non-anchored cell wall protein-6	-2.48
GO:0006355	NCU00090^‡ ‡ Genes presenting binding motif for PAC-3 in their promoter region. ^† † Transcription factors	PH-response transcription factor pacC/RIM101	-1.80
GO:0045013	NCU03965^‡ ‡ Genes presenting binding motif for PAC-3 in their promoter region.	Catabolite repression protein creC	-1.78
GO:0072344	NCU03367^‡ ‡ Genes presenting binding motif for PAC-3 in their promoter region.	Hypothetical protein	-1.78
GO:0005619	NCU08791^‡ ‡ Genes presenting binding motif for PAC-3 in their promoter region.	Catalase-1	-1.64			-2.12
GO:0048315
GO:0061414	NCU02142^‡ ‡ Genes presenting binding motif for PAC-3 in their promoter region. ^† † Transcription factors	Zn(2)-C6 fungal-type domain-containing protein	-1.55		-4.62	-4.27
GO:0030968	NCU02235^‡ ‡ Genes presenting binding motif for PAC-3 in their promoter region.	Glycosyl hydrolase family 47-6		-6.03
GO:0006355	NCU01931^‡ ‡ Genes presenting binding motif for PAC-3 in their promoter region.	Hypothetical protein		-1.98
GO:0006357
GO:0030435	NCU00399^‡ ‡ Genes presenting binding motif for PAC-3 in their promoter region.	Cell wall protein PhiA		-1.79
GO:0007264	NCU02167^‡ ‡ Genes presenting binding motif for PAC-3 in their promoter region.	Krev-1-like		-1.57
Unannotated	NCU01064^‡ ‡ Genes presenting binding motif for PAC-3 in their promoter region.	Hypothetical protein	-8.84	-5.77
GO:1902600	NCU05046^‡ ‡ Genes presenting binding motif for PAC-3 in their promoter region.	E1-E2 ATPase-1	-6.77	-5.72
GO:0055114	NCU04452^‡ ‡ Genes presenting binding motif for PAC-3 in their promoter region.	Menadione induced gene-3	-5.18	-5.77
GO:1902600	NCU07966^‡ ‡ Genes presenting binding motif for PAC-3 in their promoter region.	Calcium-transporting ATPase 3	-4.00	-3.88
GO:0009277	NCU07253^‡ ‡ Genes presenting binding motif for PAC-3 in their promoter region.	1,3-beta-glucanosyltransferase gel1	-3.56	-3.26
GO:0016787	NCU07117^‡ ‡ Genes presenting binding motif for PAC-3 in their promoter region.	Ornithine-N5-oxygenase	-3.02	-2.28
GO:0061414	NCU00155^‡ ‡ Genes presenting binding motif for PAC-3 in their promoter region. ^† † Transcription factors	C6 transcription factor	-2.10	-1.86

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[1] Send correspondence to Nilce Maria Martinez-Rossi. Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Genética, Av. Bandeirantes, 3900, 14049-900, Ribeirão Preto, SP, Brazil. E-mail: nmmrossi@usp.br.