RNA-seq of life stages of the oomycete Phytophthora infestans reveals dynamic changes in metabolic, signal transduction, and pathogenesis genes and a major role for calcium signaling in developmentReport as inadecuate




RNA-seq of life stages of the oomycete Phytophthora infestans reveals dynamic changes in metabolic, signal transduction, and pathogenesis genes and a major role for calcium signaling in development - Download this document for free, or read online. Document in PDF available to download.

BMC Genomics

, 18:198

Eukaryote microbial genomics

Abstract

BackgroundThe oomycete Phytophthora infestans causes the devastating late blight diseases of potato and tomato. P. infestans uses spores for dissemination and infection, like many other filamentous eukaryotic plant pathogens. The expression of a subset of its genes during spore formation and germination were studied previously, but comprehensive genome-wide data have not been available.

ResultsRNA-seq was used to profile hyphae, sporangia, sporangia undergoing zoosporogenesis, motile zoospores, and germinated cysts of P. infestans. Parallel studies of two isolates generated robust expression calls for 16,000 of 17,797 predicted genes, with about 250 transcribed in one isolate but not the other. The largest changes occurred in the transition from hyphae to sporangia, when >4200 genes were up-regulated. More than 1350 of these were induced >100-fold, accounting for 26% of total mRNA. Genes encoding calcium-binding proteins, cation channels, signaling proteins, and flagellar proteins were over-represented in genes up-regulated in sporangia. Proteins associated with pathogenicity were transcribed in waves with subclasses induced during zoosporogenesis, in zoospores, or in germinated cysts. Genes involved in most metabolic pathways were down-regulated upon sporulation and reactivated during cyst germination, although there were exceptions such as DNA replication, where transcripts peaked in zoospores. Inhibitor studies indicated that the transcription of two-thirds of genes induced during zoosporogenesis relied on calcium signaling. A sporulation-induced protein kinase was shown to bind a constitutive Gβ-like protein, which contributed to fitness based on knock-down analysis.

ConclusionsSpore formation and germination involves the staged expression of a large subset of the transcriptome, commensurate with the importance of spores in the life cycle. A comparison of the RNA-seq results with the older microarray data indicated that information is now available for about twice the number of genes than before. Analyses based on function revealed dynamic changes in genes involved in pathogenicity, metabolism, and signaling, with diversity in expression observed within members of multigene families and between isolates. The effects of calcium signaling, a spore-induced protein kinase, and an interacting Gβ-like protein were also demonstrated experimentally. The results reveal aspects of oomycete biology that underly their success as pathogens and potential targets for crop protection chemicals.

KeywordsOomycete Spore development Zoospore Gene regulation Transcriptomics AbbreviationsAAPAmino acid auxin permease transporter

ACAOAcyl-CoA oxidase

ACATAcyl-coA acetyl transferase

ACDHAcyl-CoA dehydrogenase

ADCAdenylate cyclase catalytic subunit

ALDFructose-bisphosphate aldolase

AMMAmmonium transporter

AP2Activating protein 2

APCAmino acid-polyamine-organocation transporter

ATSAmino acid-tRNA synthetase

BZPBasic leucine zipper

CABMo25-CAB39 family

CACCalcium channel

CADCadherin

CAMCalmodulin

CANCalcium-regulated nucleotidase

CAPCalcineurin

CAPCalcium-regulated protein phosphatase calcineurin

CARCalreticulin

CATCatalase

CDKCalcium-regulated protein kinase

CENCentrin

CH2C2H2 transcription factor

CKCasein kinase

CMGCMGC protein kinase

CMKCalmodulin-regulated protein kinase

CNGCyclic nucleotide gated ion channel

CPMCounts per million

CPTCarnitine palmitoyltransferase

CtThreshold cycle

CWDECell wall degrading enzyme

DYNDynamin

E2FWinged helix domain

ECHDEnoyl-CoA hydratase

EFHOther EF-hand protein

ELOTranslation elongation factor

ENOLEnolase phosphopyruvate hydratase

FATSodium-translocating F-ATPase

FBPFructose-1,6-bisphosphatase

FCPAspartate-based phosphatase

FDRFalse discovery rate

FPFFlagella protofilament ribbon

FPK6-phosphofructokinase

FPKMFragments per kilobase per million mapped reads

GAPDHGlyceraldehyde-3-phosphate dehydrogenase

GLKGlucokinase

GOGene ontology

GPHGlycoside-pentoside-hexuronide transporter

GPIGlucose-6-phosphate isomerase

GPXGlutathione peroxidase

GRXGlutaredoxin

GSRGlutathione reductase

GSTGlutathione S-transferase

HADHHydroxy acyl-CoA dehydrogenase

HELDNA helicase

HLHHelix-loop helix

HOMHomeodomain

HSFHeat shock factor

HTHHelix-turn-helix

INITranslation initiation factors

IRKInward rectifier potassium channel

KCSProtein kinase catalytic subunit with cNMP domain

KRSAdenylate kinase regulatory subunit

KVGPotassium voltage-gated channel

LIGDNA ligase

MCMMinichromosome maintenance protein

MEDTranscription mediator

MFSMajor facilitator superfamily with sugar domain

MSIMechanosensitive ion channel

MYBMyeloblastosis transcription factor

NFYNuclear transcription factor Y

NITNitrate transporter

ORCOrigin replication complex protein

OTHOther protein kinase

PC2Polycystin 2

PCAPrincipal component analysis

PDEPhosphodiesterase

PEPCKPhosphoenolpyruvate carboxykinase

PFK26-Phosphofructose-2-kinase

PGKPhosphoglycerate kinase

PGMPhosphoglycerate mutase

PHOPhosphate transporter

PLCPhospholipase C

POLDNA polymerase

PPDKPyruvate phosphate dikinase

PPMMetallo-dependent protein phosphatase

PPPPhosphoprotein phosphatase

PRIPrimase

PRXPeroxiredoxin

PTPProtein tyrosine phosphatase

PYCPyruvate carboxylase

PYKPyruvate kinase

RELTranslation release factors

RPRibosomal proteins

RPORNA polymerase subunit

RT-qPCRreverse transcription quantitative polymerase chain reaction

STESterile 20 kinase

SULSulfate transporter

SWTSWEET transporter

TAZTranscription adaptor putative zinc finger

TKLTyrosine kinase-like protein kinase

TMMTrimmed mean of M-values

TOPTopoisomerase

TPITriosephosphate isomerase

TRPTransient receptor potential channel

TRRThioredoxin reductase

TRXThioredoxin

TUBTubby transcription factor

Electronic supplementary materialThe online version of this article doi:10.1186-s12864-017-3585-x contains supplementary material, which is available to authorized users.

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Author: Audrey M. V. Ah-Fong - Kyoung Su Kim - Howard S. Judelson

Source: https://link.springer.com/



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