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Korean J Parasitol > Volume 59(1):2021 > Article
Moon, Park, Chu, Quan, and Kong: Differentially Expressed Gene Profile of Acanthamoeba castellanii Induced by an Endosymbiont Legionella pneumophila


Legionella pneumophila is an opportunistic pathogen that survives and proliferates within protists such as Acanthamoeba spp. in environment. However, intracellular pathogenic endosymbiosis and its implications within Acanthamoeba spp. remain poorly understood. In this study, RNA sequencing analysis was used to investigate transcriptional changes in A. castellanii in response to L. pneumophila infection. Based on RNA sequencing data, we identified 1,211 upregulated genes and 1,131 downregulated genes in A. castellanii infected with L. pneumophila for 12 hr. After 24 hr, 1,321 upregulated genes and 1,379 downregulated genes were identified. Gene ontology (GO) analysis revealed that L. pneumophila endosymbiosis enhanced hydrolase activity, catalytic activity, and DNA binding while reducing oxidoreductase activity in the molecular function (MF) domain. In particular, multiple genes associated with the GO term ‘integral component of membrane’ were downregulated during endosymbiosis. The endosymbiont also induced differential expression of various methyltransferases and acetyltransferases in A. castellanii. Findings herein are may significantly contribute to understanding endosymbiosis of L. pneumophila within A. castellanii.

Acanthamoeba spp. is one of the most abundant protozoan in the environment and commonly isolated from soil and water. Acanthamoeba spp. trophozoite usually feeds on bacteria, fungi, algae or small organic particles by phagocytosis [1]. However, some bacteria have developed strategies to resist phagocytosis, survive intracellularly and exploit Acanthamoeba spp. for multiplication [2]. These bacteria are able to survive in encysted Acanthamoeba spp. which protects the endosymbionts from adverse environmental conditions [3]. Acanthamoeba spp. not only enables the endosymbionts to persist in the environment but also enhances its pathogenicity [4]. Moreover, since mammalian macrophages and amoebae show similar interactions with endosymbionts, investigating the endosymbiotic relationship between intracellular pathogens and Acanthamoeba spp. would contribute to understanding how these organisms behave in the mammalian cells and its evasion of the human immune system.
Acanthamoeba spp. can be a host for a wide range of pathogenic microorganisms such as Legionella pneumophila, Chlamydophila pneumoniae, Cryptococcus neoformans, Mycobacterium avium, Listeria monocytogenes, and Pseudomonas aeruginosa, etc [3,57]. Among these microorganisms, the interaction between Acanthamoeba spp. and Legionella spp. is one of the most investigated. After uptake of Legionella spp. by Acanthamoeba spp., Legionella spp. forms a specialized compartment called Legionella-containing vacuole (LCV). LCV avoids fusion with lysosomes to deter lysosomal digestion and also inhibits phagosomal maturation, thereby enabling L. pneumophila to actively replicate inside the LCV [8].
To date, LCV and a large number of effectors transferred by the intracellular multiplication/defective organelle transport (Icm/Dot) type IV system of Legionella spp. have been identified [912]. Although the roles of these genes from Legionella spp. have been evaluated, little research has been done on genes of Acanthamoeba spp. during endosymbiosis with Legionella spp. To understand the intracellular survival strategy of Legionella spp., inhibition of phagosome lysis in Acanthamoeba spp. needs to be studied. In this study, total transcriptional changes of A. castellanii in response to survival and replication of L. pneumophila during 12 hr and 24 hr were investigated by RNA sequencing analysis.
The LCV in the Legionella-infected A. polyphaga has been reported to remain intact for up to 8 hr post-infection (hr pi), disrupted by 12 hr pi, and eventually lysed to release the intracellular pathogens into the cytoplasm of the amoeba by 18 to 24 hr pi [13]. L. pneumophila infection incurred the lysis of more than 80% of A. polyphaga at 24 hr pi, and it has also been suggested that the intracellular condition may significantly differ between 12–18 hr pi and 24 hr pi [13]. Contrary to the previous findings, L. pneumophila-infected A. castellanii in the present study remained intact even at 24 hr pi. Therefore, gene expression patterns at 12 hr pi and 24 hr pi were compared to confirm whether drastic differences were present in L. pneumophila-infected A. castellanii at these 2 time points.
A. castellanii was infected with L. pneumophila [14], and the Legionella-infected Acanthamoeba (L+A) was incubated for 12 hr and 24 hr at 25°C incubator. mRNA-Seq reads were mapped using TopHat software [15], and differentially expressed gene were determined based on BEDtools and EdgeR [1618]. And we used the FPKM (fragments per kilobase of exon per million fragments) as the method of determining the expression level of the gene regions. Gene classification was based on searches done by DAVID (http://david.abcc.ncifcrf.gov/).
RNA samples from different experimental conditions were sequenced to investigate the endosymbiosis-induced gene expression changes in A. castellanii (Fig. 1). A total of 7,108 genes whose expressions changed 12 hr pi and 24 hr pi were displayed using a heat map (Fig. 1A). Genes from each group were colorized based on their expression level. Strongly upregulated/downregulated genes, as indicated by intense red/blue colors, were more prevalent in the 12 hr pi group than the 24 hr pi group. Genes whose expression levels changed more than 2 fold were selected for further analysis (Fig. 1B). Among the 7,018 genes, 1,211 and 1,131 genes in the 12 hr pi group were upregulated and downregulated more than 2 fold, respectively. Similarly, 1,321 and 1,379 genes from the 24 hr pi group were upregulated and downregulated more than 2 fold, each respectively. Venn diagram revealed that a fraction of the DEGs found in the 12 hr pi overlapped with the DEGs from 24 hr pi group (Fig. 1C). Our results revealed that 2,342 and 2,700 DEGs in L. pneumophila-infected A. castellanii at 12 hr pi and 24 hr pi were changed more than 2 fold, respectively. More DEGs were observed at 24 hr pi than at 12 hr pi, which may indicate that more gene involvement is required for survival of L. pneumophila in the later stages of infection.
DEGs of L. pneumophila-infected A. castellanii were assigned an Entrez Gene ID and subsequently classified into 3 domains: biological process (BP), cellular component (CC), and molecular function (MF). Classified DEGs were subdivided further into various gene ontology (GO) terms under each of the domains. In the 12 hr pi group, DEGs were assigned to 10 subcategories in BP, 8 subcategories in CC, and 23 subcategories in MF (Fig. 2). During the 12 hr endosymbiosis, 17 genes in ‘regulation of transcription’ (domain: BP), 30 genes in the ‘nucleus’ (domain: CC), and 37 genes in ‘DNA binding’ (domain: MF) were determined to be the most upregulated genes. Within the CC domain, 200 downregulated genes were involved in the GO term ‘integral component of the membrane’. In the 24 hr pi group, DEGs were subdivided into 29, 13, and 41 GO terms under BP, CC, and MF domains, each respectively (Fig. 3). In the BP domain, 26, 39, and 32 genes from the GO terms ‘regulation of transcription’, ‘intracellular signal transduction’, and ‘cyclic nucleotide biosynthetic process’ were drastically downregulated, each respectively. In the CC domain, similar to the 12 hr pi A. castellanii, 270 downregulated genes were involved in the GO term ‘integral component of membrane’. In the MF domains, downregulated genes associated with the GO terms ‘zinc ion binding’ and ‘protein kinase activity’ were 57 and 42, respectively. From each of the domains, 26 genes from ‘carbohydrate metabolic process’ (domain: BP), 30 genes from the ‘nucleus’ (domain: CC), and 40 genes from ‘DNA binding’ (domain: MF) were mainly upregulated.
DEGs from A. castellanii, which were upregulated or downregulated more than 10 fold post-infection with L. pneumophila, were listed in Tables 1 and 2. In the 12 hr pi A. castellanii, 47 out of 1,211 DEGs were upregulated (Table 1) and 90 out of 1,131 DEGs were downregulated more than 10 fold (Table 2). Identities for several most upregulated proteins in this group were 2 hypothetical proteins (1,100 fold and 345 fold), S-adenosylmethionine-dependent methyltransferases (173 fold), and GDPD-mannose-3′, 5′-epimerase (87 fold) (Table 1). GO analysis of the assigned Entrez Gene IDs revealed that the DEG which underwent 1,100 fold increase was a hypothetical protein that belonged to the DNA binding (GO: 0003677) category. Similarly, the GDPD-mannose-3′,5′-epimerase which was increased 87 fold, was associated with catalytic activity (GO: 0003824). Based on these findings, it can be speculated that these DEGs may be of importance during the initial phase of infection. While xylosyltransferase 1 was downregulated more than 700 fold, sulfiredoxin 1 was downregulated more than 500 fold, and vacuolar sorting-associated protein 13 were downregulated more than 12 fold. (Table 2). GO analysis results revealed that the DEGs downregulated 10 fold or more were predominantly associated with the integral component of membrane (GO: 0016021). Findings are consistent with the changes in DEGs categorized under CC as illustrated in Fig. 3.
Although 132 out of 1,321 DEGs were upregulated and 54 out of 1,379 DEGs were downregulated more than 10 fold in A. castellanii 24 hr pi, approximately 60% of these DEGs (78 DEGs and 30 DEGs) were identified as hypothetical proteins. Strong inhibition of DEGs were observed in both 12 hr pi A. castellanii (90 DEGs) and 24 hr pi A. castellanii (53 DEGs). Among the DEGs demonstrating 10 fold or greater changes, 47 genes were upregulated while 90 genes were downregulated within the initial 12 hr pi (Tables 1, 2). Conversely, by 24 hr pi, 132 upregulated and 54 downregulated DEGs were observed. From these results, we supposed that L. pneumophila infection facilitated reduced A. castellanii gene expression during the early stage of infection to inhibit phagocytic digestion, while enhancing the expression of specialized A. castellanii genes during the late infection stage for LCV lysis and access to host cell machinery for intracellular replication.
Interestingly, L. pneumophila-infected A. castellanii showed differential expressions of methyltransferase-associated proteins. In addition to the S-adenosylmethionine-dependent methyltransferases and lysine methyltransferase enzyme domain-containing protein (Table 1), 11 DEGs associated with methyltransferase were upregulated, and 19 DEGs were downregulated upon infection with L. pneumophila for 12 hr. Furthermore, L. pneumophila-infected A. castellanii also demonstrated differential expressions of acetyltransferase-associated proteins. Histone acetyltransferase-associated protein was upregulated and 8 other acetyltransferases were downregulated 12 hr pi with L. pneumophila. Icm/Dot type IV secretion system and its effectors of L. pneumophila modulate host gene expression by altering the chromatin structure or by affecting the activities of transcription factors [19]. Post-translational modifications such as DNA methylation, histone acetylation, and histone methylation have been shown to play a critical role in the epigenetic regulation of eukaryotic gene expression [19,20]. Our results revealed that L. pneumophila-infected A. castellanii showed differential expressions of 30 kinds of methyltransferase-associated proteins and 9 kinds of acetyltransferase-associated proteins at 12 hr pi. Based on the changes to epigenetic regulatory gene expressions, it can be speculated that L. pneumophila can alter the gene expression of A. castellanii through epigenetic mechanisms.
A plethora of DEGs induced in A. castellanii by the endosymbiont L. pneumophila were revealed in this study. However, 38.3% (1,930 of the 5,042) of A. castellanii genes were identified to be hypothetical proteins. Proportions of theses hypothetical proteins in the 12 and 24 hr pi groups can be ascribed to the lack of Acanthamoeba spp. database. Our investigation of the DEGs in A. castellanii by an endosymbiont provides important information to understanding the survival strategy utilized by notable intracellular pathogen L. pneumophila in A. castellanii. Future studies investigating the presence of an endosymbiosis-specific gene may help elucidate the underlying mechanism involved in L. pneumophila pathogenesis, which would contribute to understanding the inhibition of phagocytosis within A. castellanii or even immune evasion mechanism in human macrophages.


This work was supported by the National Research Foundation of Korea (NRF) grant funded by Korea government (MIST) (No. 2020R1F1A1068719).


The authors declare that they have no conflict of interest.


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Fig. 1
An overview of significant changes in the gene expression profiles of A. castellanii. (A) Gene expressions under different experimental conditions displayed using a heat map. (B) The number of genes with significantly increased or decreased expression (more than 2 fold). (C) Venn diagram showing the number of overlapping genes differentially expressed among 3 experimental conditions. L+A(12 hr)/A; L. pneumohpila infected A. castellanii for 12 hr/A. castellanii, L+A(24 hr)/A; L. pneumohpila infected A. castellanii for 24 hr/A. castellanii, L+A(24 hr)/L+A(12 hr); L. pneumohpila infected A. castellanii for 24 hr/L. pneumohpila infected A. castellanii for 12 hr.
Fig. 2
Distribution of gene ontology (GO) functional classifications. GO analysis of downregulated (left-hand direction) and upregulated (right-hand direction) genes in A. castellanii infected with L. pneumophila after 12 hr.
Fig. 3
Distribution of gene ontology (GO) functional classifications. GO analysis of downregulated (left-hand direction) and upregulated (right-hand direction) genes in A. castellanii infected with L. pneumophila after 24 hr.
Table 1
Genes upregulated more than 10 fold in A. castellanii 12 hr pi
Gene symbol Fold change Annotation GO analysis

L+A(12)/A L+A(24)/A Product Category (Term)
ACA1_328910 1099.734 136.04 hypothetical protein MF (GO:0003677)

ACA1_183610 345.332 0.920 hypothetical protein -

ACA1_183700 173.774 0.462 S-adenosylmethionine-dependent methyltransferases -

ACA1_140050 116.896 15.154 hypothetical protein CC (GO:0016021)

ACA1_183570 87.745 0.232 GDPD-mannose-3′,5′-epimerase MF (GO:0003824)

ACA1_324870 66.918 38.929 hypothetical protein -

ACA1_300830 61.232 23.274 permeases of the major facilitator superfamily CC (GO:0016021)

ACA1_139940 51.100 7.577 hypothetical protein -

ACA1_183970 50.688 0.239 hypothetical protein CC (GO:0016021)

ACA1_264780 41.374 2.313 hypothetical protein -

ACA1_159010 36.741 11.383 NmrAlike family protein -

ACA1_098380 27.710 0.838 hypothetical protein -

ACA1_248200 25.965 3.365 phosphotransferase enzyme domain containing protein -

ACA1_183940 25.733 0.905 GTPase activating Rap/RanGAP domainlike 3, putative -

ACA1_096640 20.427 7.341 hypothetical protein -

ACA1_183760 17.942 0.999 lysine methyltransferase enzyme domain containing protein -

ACA1_376940 17.875 3.938 BNR/Aspbox repeat domain containing protein -

ACA1_183580 17.602 0.724 S-adenosylmethionine-dependent methyltransferases -

ACA1_270170 15.076 1.686 von Willebrand factor type A domain containing protein -

ACA1_158840 15.058 6.332 metal dependent phosphohydrolase -

ACA1_289630 14.765 11.367 hypothetical protein -

ACA1_381540 14.601 0.503 hypothetical protein -

ACA1_224160 14.371 6.761 Sec23/Sec24 beta-sandwich domain containing protein -

ACA1_175370 14.029 6.388 Erf4 domain containing protein CC (GO:0016021)

ACA1_140540 13.733 6.286 MORN repeatcontaining protein -

ACA1_184710 13.687 26.561 Phospholipid methyltransferase domain containing protein CC (GO:0016021)

ACA1_068540 13.266 5.034 Prokumamolisin, activation domain containing protein -

ACA1_217750 13.172 4.030 phosphoenolpyruvate carboxykinase (GTP), putative MF (GO:0016301)

ACA1_116700 13.149 9.620 hypothetical protein -

ACA1_279740 12.960 5.501 hydrogenase assembly factor, putative MF (GO:0051536)

ACA1_116690 12.553 5.917 hypothetical protein CC (GO:0016021)

ACA1_285180 12.470 58.313 DNA breaking-rejoining enzyme domain containing protein MF (GO:0003677)

ACA1_215790 12.170 8.113 copper/zinc superoxide dismutase -

ACA1_275740 12.097 4.360 glycerol-3-phosphate dehydrogenase (soluble) MF (GO:0051287)

ACA1_058320 12.094 4.914 GPR1/FUN34/yaaH family protein CC (GO:0016021)

ACA1_358270 11.433 7.344 pyridine nucleotidedisulfide oxidoreductase domain containing protein MF (GO:0016491)

ACA1_067720 11.300 8.046 hypothetical protein -

ACA1_153710 11.001 0.845 RFX_DNA_binding BP (GO:0006355)

ACA1_091110 10.950 0.842 hypothetical protein -

ACA1_256560 10.936 3.671 hypothetical protein -

ACA1_275730 10.900 2.743 phosphoglycerate mutase family domain containing protein -

ACA1_165640 10.762 1.971 hypothetical protein -

ACA1_060580 10.631 4.515 phosphatase -

ACA1_245710 10.555 7.545 hypothetical protein -

ACA1_325450 10.443 4.372 CBS domain containing protein -

ACA1_187310 10.274 6.715 heme NO binding domain containing protein -

ACA1_238590 10.109 3.454 CBS domain containing protein -
Table 2
Genes downregulated more than 10 fold in A. castellanii 12 hr pi
Gene symbol Fold change Annotation GO analysis

L+A(12)/A L+A(24)/A Product Category (Term)
ACA1_113420 0.001 0.764 hypothetical protein -

ACA1_112520 0.001 0.493 Cysteine-rich 4 helical bundle widely conserved -

ACA1_111980 0.003 0.368 EF hand domain containing protein -

ACA1_112090 0.003 0.454 hypothetical protein -

ACA1_111740 0.007 0.190 hypothetical protein -

ACA1_112480 0.007 0.492 Fbox domain containing protein -

ACA1_376130 0.007 0.386 xylosyltransferase 1, putative -

ACA1_058410 0.009 0.019 hypothetical protein -

ACA1_147740 0.010 0.006 CBS domain containing protein -

ACA1_113310 0.013 0.765 hypothetical protein -

ACA1_166550 0.017 0.318 hypothetical protein -

ACA1_374390 0.018 0.924 hypothetical protein -

ACA1_101570 0.019 1.673 hypothetical protein -

ACA1_392590 0.020 0.401 hypothetical protein -

ACA1_060120 0.021 0.548 hypothetical protein -

ACA1_400130 0.021 0.021 hypothetical protein -

ACA1_307550 0.022 0.084 Fbox domain containing protein -

ACA1_230230 0.022 0.022 hypothetical protein -

ACA1_050390 0.024 2.233 3-oxoacyl-[acyl-carrier protein] reductase CC (GO: 0016021)

ACA1_112110 0.024 0.463 glycosyl transferase CC (GO: 0016021)

ACA1_112490 0.024 0.480 hypothetical protein -

ACA1_063680 0.026 0.072 Reverse transcriptase -

ACA1_390590 0.027 0.132 Hsp20/alpha crystallin superfamily protein -

ACA1_063960 0.029 0.078 hypothetical protein -

ACA1_112130 0.029 0.457 regulator of g protein signaling domain containing protein -

ACA1_111970 0.029 0.399 sulfiredoxin 1 -

ACA1_158820 0.029 0.646 hypothetical protein -

ACA1_064370 0.029 0.029 AT Hook plus PHD finger transcription factor family member (athp1), putative -

ACA1_064780 0.029 0.029 hypothetical protein -

ACA1_064790 0.029 0.029 hypothetical protein -

ACA1_340040 0.030 0.275 zinc finger, zz type domain containing protein -

ACA1_350050 0.030 0.298 hypothetical protein -

ACA1_112530 0.031 0.499 NLPC_P60 super family -

ACA1_112180 0.032 0.527 major facilitator subfamily transporter CC (GO: 0016021)

ACA1_112590 0.034 0.474 WH2 motif domain containing protein -

ACA1_050380 0.036 1.885 hypothetical protein -

ACA1_230220 0.037 0.025 hypothetical protein -

ACA1_199000 0.038 0.229 SnoaL-like domain containing protein -

ACA1_077210 0.040 0.376 hypothetical protein -

ACA1_173000 0.043 0.352 Predicted NAD/FAD-dependent oxidoreductase -

ACA1_326260 0.043 0.073 hypothetical protein -

ACA1_060740 0.045 0.310 hypothetical protein -

ACA1_270160 0.046 0.071 fascin subfamily protein -

ACA1_200180 0.048 0.428 hypothetical protein -

ACA1_383480 0.051 0.029 hypothetical protein -

ACA1_155760 0.052 0.145 phosphoribosyltransferase -

ACA1_207830 0.052 0.426 myotubularins and other putative membrane-associated proteins -

ACA1_133180 0.052 0.254 Ser/Thr phosphatase family superfamily protein -

ACA1_077290 0.053 0.638 5′nucleotidase CC (GO: 0016021)

ACA1_365080 0.053 0.367 hypothetical protein -

ACA1_383650 0.055 0.349 Human glyoxalase domain-containing protein 5 and similar proteins -

ACA1_048480 0.056 0.616 hypothetical protein -

ACA1_055330 0.059 0.292 N-terminal region of Chorein or VPS13 -

ACA1_346470 0.060 0.450 RUN domain containing protein -

ACA1_298420 0.062 0.056 hypothetical protein -

ACA1_197730 0.064 0.823 hypothetical protein -

ACA1_378930 0.064 0.329 hypothetical protein -

ACA1_214630 0.067 0.147 hypothetical protein CC (GO: 0016021)

ACA1_128200 0.068 0.051 CBS domain containing protein -

ACA1_052800 0.071 0.571 O-methyltransferase family 3 protein -

ACA1_112560 0.071 0.499 hypothetical protein -

ACA1_322750 0.072 0.552 Glycosyl hydrolases family 2, TIM barrel domain -

ACA1_383400 0.072 1.376 hypothetical protein CC (GO: 0016021)

ACA1_253630 0.073 0.947 hypothetical protein -

ACA1_391470 0.074 0.821 Hsp20/alpha crystallin superfamily protein -

ACA1_066110 0.074 0.05 SCP-like extracellular protein domain containing protein -

ACA1_131790 0.075 0.133 protein from patent family protein -

ACA1_111930 0.075 0.311 carbonsulfur lyase, putative BP (GO: 0008152)

ACA1_064380 0.077 0.052 hypothetical protein -

ACA1_064940 0.077 0.029 Fbox domain containing protein -

ACA1_323370 0.077 0.011 Hsp20/alpha crystallin superfamily protein -

ACA1_383750 0.078 0.236 Ubiquitinconjugating enzyme subfamily protein -

ACA1_006080 0.079 0.210 hypothetical protein CC (GO: 0016021)

ACA1_180590 0.082 0.546 TRRAP family protein -

ACA1_112980 0.083 0.755 protein kinase -

ACA1_077300 0.083 0.247 serine/threonine kinase CC (GO: 0016021)

ACA1_111880 0.084 0.225 Small acidic protein family -

ACA1_372720 0.084 0.148 obtusifoliol 14alphademethylase, putative CC (GO: 0016021)

ACA1_046720 0.086 0.076 Glycosyl hydrolase families -

ACA1_324050 0.088 0.646 Vacuolar sorting-associated protein 13 [Intracellular trafficking and secretion] -

ACA1_400540 0.088 0.076 sphingosine hydroxylase CC (GO: 0016021)

ACA1_290200 0.089 0.329 hypothetical protein -

ACA1_389110 0.09 1.016 hypothetical protein -

ACA1_112500 0.094 0.535 TBC domain containing protein -

ACA1_311650 0.095 0.096 hypothetical protein -

ACA1_112060 0.096 0.429 O-methyltransferase, putative -

ACA1_178260 0.097 0.118 cytochrome P450, putative MF (GO: 0005506)

ACA1_066960 0.098 1.036 hypothetical protein -

ACA1_046710 0.099 0.126 cytoplasmic protein, putative -

ACA1_112640 0.100 0.498 MBOAT family protein CC (GO: 0016021)
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