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Amino acid substitutions in specific proteins correlate with farnesol unresponsiveness in Candida albicans

BMC Genomics volume 24, Article number: 93 (2023) Cite this article

Abstract

Background

The quorum-sensing molecule farnesol, in opportunistic yeast Candida albicans, modulates its dimorphic switch between yeast and hyphal forms, and biofilm formation. Although there is an increasing interest in farnesol as a potential antifungal drug, the molecular mechanism by which C. albicans responds to this molecule is still not fully understood.

Results

A comparative genomic analysis between C. albicans strains that are naturally unresponsive to 30 µM of farnesol on TYE plates at 37 °C versus responsive strains uncovered new molecular determinants involved in the response to farnesol. While no signature gene was identified, amino acid changes in specific proteins were shown to correlate with the unresponsiveness to farnesol, particularly with substitutions in proteins known to be involved in the farnesol response. Although amino acid changes occur primarily in disordered regions of proteins, some amino acid changes were also found in known domains. Finally, the genomic investigation of intermediate-response strains showed that the non-response to farnesol occurs gradually following the successive accumulation of amino acid changes at specific positions.

Conclusion

It is known that large genomic changes, such as recombinations and gene flow (losses and gains), can cause major phenotypic changes in pathogens. However, it is still not well known or documented how more subtle changes, such as amino acid substitutions, play a role in the adaptation of pathogens. The present study shows that amino acid changes can modulate C. albicans yeast’s response to farnesol. This study also improves our understanding of the network of proteins involved in the response to farnesol, and of the involvement of amino acid substitutions in cellular behavior.

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Background

The yeast Candida albicans is normally a harmless commensal organism [1]. However, it can also be an opportunistic fungal pathogen in humans, causing a wide range of diseases from superficial mucosal infections to life-threatening systemic disorders [2, 3]. For example, C. albicans is the main causative agent of thrush in up to 95% of cases of oral yeast infections [4]. In addition, vulvovaginal candidiasis is a common mucosal infection caused mainly by C. albicans, which afflicts roughly 75% of women at least once in their lifetime [5]. Depending on the environmental conditions, C. albicans can grow in three main cellular morphologies: yeast as ovoid budding cells, hyphae as branching filamentous cells, and pseudohyphae as constricted chains of yeast cells. The ability of C. albicans to colonize or cause an infection depends on several virulence factors and traits, such as biofilm formation and the dimorphic switch between yeast and hyphal forms [6]. For several pathogens, including C. albicans, the formation of biofilms allows the yeast to get past host defenses, which can cause recalcitrant infections [7,8,9,10].

Quorum sensing (QS) is a strategy used by many microorganisms to assess population density through the production and sense of autoinducers [11]. QS in fungi is particularly important since it controls several intra- and inter-species mechanisms and behaviors, such as morphogenesis, sexual differentiation, and virulence [12, 13]. C. albicans is known to produce various QS molecules that regulate the morphogenetic process [11, 14]. Fungi and yeasts can also alter host immune cell recognition and response with QS molecules [15], but QS molecules with above-threshold concentrations can induce fungal apoptosis [13].

Farnesol, a precursor of the isoprenoid sterol that regulates germination, is the best-described QS molecule produced by C. albicans [16]. Farnesol has been shown to inhibit the yeast-to-mycelium conversion when it accumulates beyond a threshold level, leading to the yeast actively budding without influencing cellular growth rates [17]. However, farnesol is unable to halt the elongation of pre-existing hyphae [18, 19]. The inhibitory effects of farnesol on hyphal transition and biofilm formation [20] demonstrated that the antibiofilm properties of farnesol are potential preventive strategies [21].

Studying the effect of farnesol on biofilm formation is complex, because farnesol inhibits hyphal formation regulating several genes in the cyclic AMP signaling pathway [22]. Although the mechanisms of response to farnesol have never been characterized thoroughly, studies have shown that various genes are involved in the resistance of C. albicans biofilms to antifungals in the presence or absence of farnesol [23, 24].

In this study, by screening a library of clinical C. albicans strains that either do not, or only partially respond to farnesol, and thus continue to produce hyphae in presence of the molecule, we discovered that some amino acid substitutions in specific proteins correlate with the alteration of the normal response to farnesol. The present study showed that some molecular determinants may participate in the response to farnesol in C. albicans, and demonstrated that subtle mutations, such as amino acid changes, can have major phenotypic repercussions in pathogens.

Results

Since yeast-to-hypha growth is a key factor in C. albicans virulence, we tested the effect of farnesol on filamentous growth in different strains. Under the growth conditions used here, we found three different phenotypes of C. albicans strains in the presence of 30 µM of farnesol, a concentration close to the one produced naturally by C. albicans [25], after 48 h (Fig. 1). In SC5314, BL007, BL077, and BL273 strains hypha formation was inhibited at 30 µM of farnesol; the colonies adopt a smooth phenotype, which is the expected phenotype for strains that are responsive (R) to the farnesol molecule [26]. Three other strains (ATCC36802, HM1, and BL266) did not respond to farnesol and kept the hairy phenotype (non-responsive, NR). Interestingly, six strains (JMN070, BL167, BL288, BL300, BL296, and BL152) adopt a partial phenotype (partially responsive, PR) that showed some extent of hyphae growth.

Fig. 1
figure 1

Three different phenotypes of C. albicans strains with or without 30 µM concentrations of farnesol. In SC5314, hyphal production was inhibited when 30 µM of farnesol is added to the solid medium (a,b). BL300 demonstrated partial hyphal production in presence of 30 µM farnesol (c,d). ATCC36802 did not respond to farnesol (e,f)

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To better understand the molecular determinants involved in the response to farnesol in C. albicans, the DNA of the studied strains was sequenced. Assembly and annotation revealed GC content, genome size, and the number of proteins similar to what was previously described for C. albicans and other species of the Candida genus (Table 1) [27,28,29].

Table 1 General information on genome assembly and annotation of C. albicans strains
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Sequences were used to examine the phylogenetic relationships of C. albicans strains (Fig. 2). The phenotypes (level of response to farnesol) are not monophyletic; the strains are scattered all over the tree. This analysis thus suggests that the difference in the level of response to farnesol is the result of convergent evolution, and was not transmitted vertically among the strains studied. Also, the lengths of the branches are relatively uniform, showing that there is no obvious correlation between the rate of evolution and the level of response to farnesol.

Fig. 2
figure 2

 A maximum likelihood tree of the C. albicans strains studied. Different strains with distinct levels of phenotypic response to farnesol are represented as colorful circles: green, complete phenotype response to farnesol (R); blue, partial phenotype response to farnesol (PR); red, no phenotype response to farnesol (NR). The boostraps values are all 100, except for one node which has a support of 97 (shown in the figure)

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A sequence homology search was performed to determine whether the unresponsiveness to farnesol could be caused by the presence or absence of one or more genes. By comparing sequences from the responsive and non-responsive strains, it was not possible to find any gene that could be a signature of the phenotype. Similarly, no point mutations in regulatory regions were found only in the genomes of non-responsive strains. A recent bioinformatics tool, CAPRIB [30], was used to verify if amino acid changes correlated with unresponsiveness to farnesol. While no marker gene was identified, a total of 38 positions in proteins of strains that respond to farnesol were found to be systematically different in strains that do not respond (Fig. 3). The 38 positions are found on 37 proteins (one of the proteins has two mutations). By investigating the sequences of strains that partially respond to farnesol, several of the 38 amino acid changes were found. However, compared to strains that have complete unresponsiveness to farnesol (NR), no partially responsive strains (PR) have all 38 amino acid changes.

Several mutations provide strong evidence for the involvement of detected proteins in the level of response to farnesol. For example, in an earlier study, ALG8 was described as a gene whose activation resulted in sensitivity to farnesol [31]. In the three strains that do not respond to farnesol and in four strains with a partial phenotype, the same substitution in Alg8p was observed. This reinforces the idea that ALG8 plays an important role in the pathway of response to farnesol.

As expected, some proteins have clear roles in hypha morphology and hypha elongation rate as farnesol has direct effects on the hypha growth of C. albicans. For example, the PMR1 gene induced a decrease in the rate of hypha elongation in yeast [32]. Therefore, identifying an amino acid substitution in Pmr1p suggested a new role for this protein as an effector of the morphological response to farnesol. In another example, a previous study showed that CCZ1 was required for filamentous development and virulence in C. albicans and was a promising target for antifungal drug development [33]. The presence of Ccz1p as a candidate protein for the response to farnesol indicated other aspects of its function. An amino acid change was also detected in Sfu1p, a protein involved in RNA biosynthesis, and whose gene is known to be downregulated in the presence of farnesol in Candida auris [34], a species close to C. albicans.

Fig. 3
figure 3

 A list of 38 amino acid substitutions was identified in 37 proteins correlating with unresponsiveness to farnesol in NR (red) and PR (blue) strains of C. albicans. The information is given according to the reference strain SC5314. Every column in the center of the matrix indicates one strain of C. albicans and the green and black boxes show the presence and absence of amino acid substitutions respectively. NR and PR strains are categorized based on the amounts of amino acid substitution that are detected among them. The white and blue rows show information about detected proteins such as name, description, length, location of the activity, chromosomal location, conserved domains, and secondary structures (SS); (H = helix, C = coil, S = strand)

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Only one amino acid change, in the Bem2p protein, is found in all NR or PR strains. Earlier studies showed that Bem2p plays significant roles in morphogenesis checkpoints, and the cooperation between Bem2p and Bem3p is essential for bud emergence [35, 36]. In contrast, two mutations in two proteins (Cta8p and Gor1p) are exclusively present in NR strains and not at all in PR strains. Cta8p and Gor1p are involved in stress responses [37] and there is currently no obvious evidence for the relevant roles of these proteins in the pathway of response to farnesol.

Evidence shows that Cpp1p of C. albicans represses hyphal gene expression and regulates morphological changes by blocking the yeast-to-hyphal transition [38]. Regardless of the clear role of Cpp1p in response to farnesol, among candidate proteins, only Cpp1p showed two different amino acid changes in PR strains.

The relation between the detected amino changes and the conserved domains of proteins can provide insight into the structural involvement of the mutations. Among the 38 substitutions that were identified, 13 were in conserved domains which indicate functionally important regions (Fig. 3). Protein function is directly related to the structure of that protein, and among the 38 detected mutations, 24 (63%) are observed at coil secondary structures. In addition, the proteins with amino acid changes are in every chromosome of C. albicans, although chromosome 7 has the most changes (see Additional file 1), with respect to the total number of proteins by chromosome.

The connections of genes that contain the mutations were analyzed through a STRING analysis. As shown in Fig. 4, some gene interactions were revealed, such as associations of ALG8, already known to be involved in response to farnesol, with PMR1, CCZ1, and MVP1. This network may indicate a part of the pathway of response to farnesol.

Fig. 4
figure 4

 A STRING analysis showing putative relationships between genes found mutated in NR strains

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Discussion

It has been demonstrated that farnesol acts as a quorum-sensing molecule that inhibits filamentation and biofilm formation in C. albicans [17]. Although studies have revealed certain molecular determinants involved in the production and response to farnesol [23, 26], the entire protein interaction network and the way C. albicans modulates its genome to respond to this molecule remain largely unknown.

We investigated genome sequences of clinical strains that respond and do not respond to farnesol to better understand, by comparative genomics, the mechanism of response to this molecule. Clinical isolates are of great interest since they reflect what happens in real life, not genetic manipulation in the laboratory. It is known that genomic plasticity, and gene flow in general, play a determining role in the diversification and evolution of C. albicans [39]. Surprisingly, according to our results, no marker gene for response or non-response to farnesol was found. This suggests that the loss of genes involved in the response to farnesol is not the mechanism preferentially selected by evolution to modulate the response for this molecule. However, as reviewed elsewhere [40], C. albicans, in addition to being able to modulate its gene repertoire, has a myriad of other mechanisms that allow it to modify its genome and thus adapt to various environments and adjust its virulence.

C. albicans has a compact genome for a eukaryote (~ 36% of coding) with strong purifying selection to preserve the integrity of the coding regions of point mutations [39]. Despite this, it has been found that non-synonymous mutations occur uniformly across the genome [41] and that genes that encode for cell surface proteins are conducive to a higher rate of mutation [42, 43]. While no gene is a marker of response or non-response to farnesol, it was possible to identify 38 amino acid substitutions that correlate with the level of response. Moreover, among the 37 proteins in which amino acid substitutions were detected, some are known to be involved in farnesol response. This is the case for ALG8, which is known to be involved in the farnesol sensitivity gene network interaction [31]. Interestingly, ALG8 is connected in a network with other genes, such as PMR1, CCZ1, MVP1, VPS36, and CAALFM_C405980CA, for which proteins have amino acid substitutions (Fig. 4). The genes PMR1 and CCZ1 have obvious roles in limiting hyphae development [33, 44] and may thus also be involved in farnesol response.

In C. albicans, farnesol affects the transcription level of several genes [45, 46]. Interestingly, conserved amino acid substitutions were found in three transcription proteins (Sfu1p, C3_02020wp (encoded by MRD1), Nup82p). The gene SFU1 is already known to downregulate in the presence of farnesol in C. auris [45]. Besides, C. albicans globally up-regulates its cellular metabolism in response to farnesol [47, 48]. Proteins found by the present study, such as those encoded by GOR1, ALG8, XKS1, AAH1, and LYS1, are also involved in cellular metabolism [49,50,51,52,53], suggesting that these proteins may impact farnesol responsiveness by having global effects on the cells.

Only one protein, Bem2p, have a conserved amino acid substitution in all strains that do not fully respond to farnesol. Two hypotheses could be proposed to explain the roles of the substitution in Bem2p for response to farnesol. On the first hand, the function of Bem2p is essential in controlling C. albicans virulence-pathogenesis in the farnesol responsiveness pathway. On the other hand, it is possible to postulate that this mutation must appear early in order to allow the other mutations. Contrarily, Cta8p and Gor1p are two proteins that showed amino acid substitutions just in NR strains, both of which may be essential for C. albicans to have complete farnesol resistance.

We expanded our mutational analysis of detected proteins by investigating conserved domains. There is evidence that mutations in conserved regions may be detrimental to the proteins [54, 55]. Some detected amino acid substitutions are located in conserved domains, such as for proteins Alg8p, Bem2p, Pmr1p, and Cpp1p. This suggests structural distortion of these proteins. In PR strains the presence of two distinct mutations in Cpp1p (Figs. 3 and 205P/S and 444 A/V) can be an example that several positions of a protein might be decisive for farnesol responsiveness. Also, 63% of the substituted residues found in this study were located in coil regions, a structure more resilient to mutations [56].

Conclusion

These new findings about genotype-phenotype associations add to the understanding of C. albicans adaptation, virulence, and pathogenicity as a whole. Comparing the genomes of clinical strains that do not respond to farnesol did not reveal any gene that was a marker of response or non-response to farnesol. However, there are amino acid substitutions that correlate with the level of phenotypic farnesol response. This demonstrates that subtle mutations, such as amino acid substitutions, can cause important phenotypes in pathogens, as recently suggested in the bacteria of the genus Mycobacterium [30]. Among proteins with amino acid substitutions, Alg8p is a known gene that plays an obvious role in the C. albicans farnesol response. Also, the connection of ALG8 with some other genes, such as PMR, CCZ1, VPS36, and MVP1 introduces potential new roles for them in mediating the C. albicans response to farnesol. Therefore, this study provides new and valuable insights not only in our understanding of the molecular pathway of response to farnesol but also may lead to investigations of novel strategies for the development of antifungal drugs. Finally, as more genomes of C. albicans strains that naturally do not respond to farnesol are sequenced, the extent of the mechanisms allowing the response to this molecule will be known ever-more precisely.

Methods

Strains, culture and farnesol responsiveness assessment

The C. albicans strains used in this study are listed in Table 2. All strains were isolated from patients of Faculté de Médecine Dentaire clinics, Université de Montréal, and graciously donated by third parties to this project. Conservation of clinical strains were made by cryopreservation in glycerol at -80 °C. For the farnesol assay, strains were thawed on Sabouraud Dextrose Agar (SDA). For each strain, single colonies of C. albicans were cultivated for 24 h without agitation at 37 °C in TYE liquid media (For 1 L: 17 g trypticase-peptone, 3 g yeast extract, 5 g sodium chloride, 2.5 g sodium phosphate dibasic anhydrous) and 1.5% (W/V) of glucose, sterilized by filtration. For farnesol response assays, cells were pelleted and washed twice with sterile saline (NaCl 0.85% (W/V)). Approximately 250 cells, determined by hemacytometer or viable count on SDA, were plated on a TYE agar with 30 µM trans, trans-farnesol (Sigma, St-Louis, MO) diluted in methanol and incubated for 48 h at 37 ˚C with 2.5% CO2. A control condition with the same volume of methanol without farnesol was also used. Farnesol response assays were repeated three times in three different cultures and the morphology of every colony was surveyed. The strains were classified based on their phenotypic response in the presence of 30 µM farnesol. Strains with more than 90% of the smooth colony were considered responsive phenotypes, strains with a stable population of more than 90% hairy colonies (i.e., with hyphal production) were considered non-responsive, and strains with 10–90% of hairy colonies on the plate were considered partially responsive (Table 2).

Table 2 Candida albicans strains used in this study
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N/A: not available in medical file or literature; Gender: male (M) or female (F); Responsive (R): strain responsive to 30 µM farnesol, more than 90% of smooth colony was observed; Non-responsive (NR): strain presenting, in a stable way, more than 90% of hairy colonies on 30 µM farnesol; Partially responsive (PR): strain with variable response to farnesol between 10 and 90% of hairy colonies.

Sequencing and bioinformatics analyses

C. albicans strains were grown on Sabouraud’s 2% dextrose agar at 30 ˚C for 72 h. Genomic DNA extraction of the 12 strains was performed using the DNeasy PowerSoil Pro extraction kit from QIAGEN, following the manufacturer’s instructions. The purified DNA samples were sequenced on an Illumina NovaSeq 6000 device by the Genome Quebec Centre of Expertise and Services (Montréal, Canada). The resulting sequencing reads of each strain were de novo assembled using MaSuRCA 4.0.9 [57]. The annotation was carried out using the funannotate pipeline 1.8.9 [58].

The sequences of the 13 strains of C. albicans (including the reference strain SC5314) were used to construct a molecular phylogeny. The complete pipeline used is described in detail elsewhere [59]. The differences are that in the present study GET_HOMOLOGUES 20,220,516 was used to find homology links and IQ-TREE 1.4.4 for phylogenetic reconstruction with 10,000 ultrafast boostraps. The final tree has been midpoint-rooted using FigTree version 1.4.3 (http://tree.bio.ed.ac.uk/software/figtree/). GET_HOMOLOGUES was also used to search for signature genes that could explain the non-response to farnesol.

The breseq tool version 0.37.1 [60] was used to identify point mutations in the regulatory regions of genes. The − 150 bp and + 150 bp regions of the genes were considered. The genome of strain SC5314 was used as a reference. The CAPRIB tool [30] was used to determine the amino acid changes that correlate with unresponsiveness to farnesol. However, BLASTP 2.12.0 was used with translated sequences annotated with funannotate instead of TBLASTN. Only proteins that share more than 85% identity and less than 1e− 10 were considered homologous. The SC5314 strain was used as a reference. Amino acid changes and strains were clustered according to a binary model in R.

The NCBI conserved domains database[61] was used to delineate the conserved domains of the studied proteins. PSIPRED 4[62] was used to generate secondary structure predictions and MEMSAT-SVM[63] to predict transmembrane regions of proteins. Functional links between proteins were detected by using STRING version 11.5 [64].

Data availability

The genomic sequences were deposited at DDBJ/ENA/GenBank under the BioProject PRJNA889397.

Abbreviations

QS:

Quorum sensing

C. albicans :

Candida albicans

DNA:

Deoxyribonucleic acid

SDA:

Sabouraud dextrose agar

TYE:

Tryptone yeast extract

References

  1. Lopes JP, Lionakis MS. Pathogenesis and virulence of Candida albicans. Virulence. 2022;13:89–121.

    Article  CAS  PubMed  Google Scholar 

  2. Kebaara BW, Langford ML, Navarathna DHMLP, Dumitru R, Nickerson KW, Atkin AL. Candida albicans Tup1 is involved in farnesol-mediated inhibition of filamentous-growth induction. Eukaryot Cell. 2008;7:980–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Kim J, Sudbery P. Candida albicans, a major human fungal pathogen. J Microbiol. 2011;49:171–7.

    Article  PubMed  Google Scholar 

  4. Vila T, Sultan AS, Montelongo-Jauregui D, Jabra-Rizk MA. Oral candidiasis: a disease of opportunity. J Fungi. 2020;6:15.

    Article  CAS  Google Scholar 

  5. Willems HME, Ahmed SS, Liu J, Xu Z, Peters BM. Vulvovaginal candidiasis: a current understanding and burning questions. J Fungi. 2020;6:27.

    Article  Google Scholar 

  6. Polke M, Leonhardt I, Kurzai O, Jacobsen ID. Farnesol signalling in Candida albicans–more than just communication. Crit Rev Microbiol. 2018;44:230–43.

    Article  CAS  PubMed  Google Scholar 

  7. Szkopińska A, Grabińska K, Delourme D, Karst F, Rytka J, Palamarczyk G. Polyprenol formation in the yeast Saccharomyces cerevisiae: Effect of farnesyl diphosphate synthase overexpression. J Lipid Res. 1997;38:962–8.

    Article  PubMed  Google Scholar 

  8. Ramage G, Walle K, Wickes BL, López-Ribot JL. Biofilm formation by Candida dubliniensis. J Clin Microbiol. 2001;39:3234–40.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Donlan RM, Costerton JW, Biofilms. Survival mechanisms of clinically relevant microorganisms. Clin Microbiol Rev. 2002;15:167–93.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Jabra-Rizk MA, Shirtliff M, James C, Meiller T. Effect of farnesol on Candida dubliniensis biofilm formation and fluconazole resistance. FEMS Yeast Res. 2006;6:1063–73.

    Article  CAS  PubMed  Google Scholar 

  11. Ge C, Sheng H, Chen X, Shen X, Sun X, Yan Y, et al. Quorum sensing system used as a tool in metabolic engineering. Biotechnol J. 2020;15:1900360.

    Article  CAS  Google Scholar 

  12. Avbelj M, Zupan J, Raspor P. Quorum-sensing in yeast and its potential in wine making. Appl Microbiol Biotechnol. 2016;100:7841–52.

    Article  CAS  PubMed  Google Scholar 

  13. Grainha TRR, Jorge PAdaS, Pérez-Pérez M, Rodríguez GP, Pereira MOBO, Lourenço AMG. Exploring anti-quorum sensing and anti-virulence based strategies to fight Candida albicans infections: an in silico approach. FEMS Yeast Res. 2018;18:foy022.

    Article  Google Scholar 

  14. Langford ML, Atkin AL, Nickerson KW. Cellular interactions of farnesol, a quorum-sensing molecule produced by Candida albicans. Future Microbiol. 2009;4:1353–62.

    Article  CAS  PubMed  Google Scholar 

  15. Abe S, Tsunashima R, Iijima R, Yamada T, Maruyama N, Hisajima T, et al. Suppression of anti-Candida activity of macrophages by a quorum-sensing molecule, farnesol, through induction of oxidative stress. Microbiol Immunol. 2009;53:323–30.

    Article  CAS  PubMed  Google Scholar 

  16. Zhu J, Krom BP, Sanglard D, Intapa C, Dawson CC, Peters BM, et al. Farnesol-induced apoptosis in Candida albicans is mediated by CDR1-p extrusion and depletion of intracellular glutathione. PLoS ONE. 2011;6:e28830.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Hornby JM, Jensen EC, Lisec AD, Tasto JJ, Jahnke B, Shoemaker R, et al. Quorum sensing in the dimorphic fungus Candida albicans is mediated by farnesol. Appl Environ Microbiol. 2001;67:2982–92.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Hornby JM, Nickerson KW. Enhanced production of farnesol by Candida albicans treated with four azoles. Antimicrob Agents Chemother. 2004;48:2305–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Mosel DD, Dumitru R, Hornby JM, Atkin AL, Nickerson KW. Farnesol concentrations required to block germ tube formation in Candida albicans in the presence and absence of serum. Appl Environ Microbiol. 2005;71:4938–40.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Henriques M, Martins M, Azeredo J, Oliveira R. Effect of farnesol on Candida dubliniensis morphogenesis. Lett Appl Microbiol. 2007;44:199–205.

    Article  CAS  PubMed  Google Scholar 

  21. Ramage G, Saville SP, Wickes BL, López-Ribot JL. Inhibition of Candida albicans biofilm formation by farnesol, a quorum-sensing molecule. Appl Environ Microbiol. 2002;68:5459–63.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Zordan RE, Galgoczy DJ, Johnson AD. Epigenetic properties of white-opaque switching in Candida albicans are based on a self-sustaining transcriptional feedback loop. Proc Natl Acad Sci U S A. 2006;103:12807–12.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Chen S, Xia J, Li C, Zuo L, Wei X. The possible molecular mechanisms of farnesol on the antifungal resistance of C. albicans biofilms: the regulation of CYR1 and PDE2. BMC Microbiol. 2018;18:1–14.

    Article  Google Scholar 

  24. Pereira R, dos Santos Fontenelle RO, de Brito EHS, de Morais SM. Biofilm of Candida albicans: formation, regulation and resistance. J Appl Microbiol. 2021;131:11–22.

    Article  CAS  PubMed  Google Scholar 

  25. Weber K, Sohr R, Schulz B, Fleischhacker M, Ruhnke M. Secretion of E,E-farnesol and biofilm formation in eight different Candida species. Antimicrob Agents Chemother. 2008;52:1852–61.

    Article  Google Scholar 

  26. Langford ML, Hargarten JC, Patefield KD, Marta E, Blankenship JR, Fanning S, et al. Candida albicans Czf1 and Efg1 coordinate the response to farnesol during quorum sensing, white-opaque thermal dimorphism, and cell death. Eukaryot Cell. 2013;12:1281–92.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Guinea J, Mezquita S, Gómez A, Padilla B, Zamora E, Sánchez-Luna M, et al. Whole genome sequencing confirms Candida albicans and Candida parapsilosis microsatellite sporadic and persistent clones causing outbreaks of candidemia in neonates. Med Mycol. 2021;60:myab068.

    Article  PubMed  Google Scholar 

  28. Szarvas J, Rebelo AR, Bortolaia V, Leekitcharoenphon P, Hansen DS, Nielsen HL, et al. Danish whole-genome-sequenced candida albicans and candida glabrata samples fit into globally prevalent clades. J Fungi. 2021;7:962.

    Article  CAS  Google Scholar 

  29. Mixão V, Hansen AP, Saus E, Boekhout T, Lass-Florl C, Gabaldón T. Whole-genome sequencing of the opportunistic yeast pathogen candida inconspicua uncovers its hybrid origin. Front Genet. 2019;10:383.

    Article  PubMed  PubMed Central  Google Scholar 

  30. Guerra Maldonado JF, Vincent AT, Chenal M, Veyrier FJ. CAPRIB: a user-friendly tool to study amino acid changes and selection for the exploration of intra-genus evolution. BMC Genomics. 2020;21:1–14.

    Article  Google Scholar 

  31. Fairn GD, MacDonald K, McMaster CR. A chemogenomic screen in Saccharomyces cerevisiae uncovers a primary role for the mitochondria in farnesol toxicity and its regulation by the Pkc1 pathway. J Biol Chem. 2007;282:4868–74.

    Article  CAS  PubMed  Google Scholar 

  32. Brand A, Lee K, Veses V, Gow NAR. Calcium homeostasis is required for contact-dependent helical and sinusoidal tip growth in Candida albicans hyphae. Mol Microbiol. 2009;71:1155–64.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Dong Y, Yu Q, Chen Y, Xu N, Zhao Q, Jia C, et al. The Ccz1 mediates the autophagic clearance of damaged mitochondria in response to oxidative stress in Candida albicans. Int J Biochem Cell Biol. 2015;69:41–51.

    Article  CAS  PubMed  Google Scholar 

  34. Silva E, Monteiro R, Grainha T, Alves D, Pereira MO, Sousa AM. Fostering innovation in the treatment of chronic polymicrobial cystic fibrosis-associated infections exploring aspartic acid and succinic acid as ciprofloxacin adjuvants. Front Cell Infect Microbiol. 2020;10:441.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Marquitz AR, Harrison JC, Bose I, Zyla TR, McMillan JN, Lew DJ. The Rho-GAP Bem2p plays a GAP-independent role in the morphogenesis checkpoint. EMBO J. 2002;21:4012–25.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Knaus M, Pelli-Gulli MP, van Drogen F, Springer S, Jaquenoud M, Peter M. Phosphorylation of Bem2p and Bem3p may contribute to local activation of Cdc42p at bud emergence. EMBO J. 2007;26:4501–13.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Sellam A, Askew C, Epp E, Lavoie H, Whiteway M, Nantel A. Genome-wide mapping of the coactivator Ada2p yields insight into the functional roles of SAGA/ADA complex in Candida albicans. Mol Biol Cell. 2009;20:2389–400.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Schröppel K, Sprößer K, Whiteway M, Thomas DY, Röllinghoff M, Csank C. Repression of hyphal proteinase expression by the mitogen-activated protein (MAP) kinase phosphatase Cpp1p of Candida albicans is independent of the MAP kinase Cek1p. Infect Immun. 2000;68:7159–61.

    Article  PubMed  PubMed Central  Google Scholar 

  39. Ene I, Bennett RJ, Anderson MZ. Mechanisms of genome evolution in Candida albicans. Curr Opin Microbiol. 2019;52:47–54.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Mba IE, Nweze EI, Eze EA, Anyaegbunam ZKG. Genome plasticity in Candida albicans: a cutting-edge strategy for evolution, adaptation, and survival. Infect Genet Evol. 2022;99:105256.

    Article  CAS  PubMed  Google Scholar 

  41. Hirakawa MP, Martinez DA, Sakthikumar S, Anderson MZ, Berlin A, Gujja S, et al. Genetic and phenotypic intra-species variation in Candida albicans. Genome Res. 2015;25:413–25.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Zhao X, Pujol C, Soll DR, Hoyer LL. Allelic variation in the contiguous loci encoding Candida albicans ALS5, ALS1 and ALS9. Microbiology. 2003;149:2947–60.

    Article  CAS  PubMed  Google Scholar 

  43. Zhao X, Oh SH, Jajko R, Diekema DJ, Pfaller MA, Pujol C, et al. Analysis of ALS5 and ALS6 allelic variability in a geographically diverse collection of Candida albicans isolates. Fungal Genet Biol. 2007;44:1298–309.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Navarro-Arias MJ, Defosse TA, Dementhon K, Csonka K, Mellado-Mojica E, Valério AD, et al. Disruption of protein mannosylation affects Candida guilliermondii cell wall, immune sensing, and virulence. Front Microbiol. 2016;7:1951.

    Article  PubMed  PubMed Central  Google Scholar 

  45. Jakab Á, Balla N, Ragyák Á, Nagy F, Kovács F, Sajtos Z, et al. Transcriptional profiling of the Candida auris response to exogenous farnesol exposure. mSphere. 2021;6:e0071021.

    Article  PubMed  Google Scholar 

  46. Cho T, Aoyama T, Toyoda M, Nakayama H, Chibana H, Kaminishi H. Transcriptional changes in Candida albicans genes by both farnesol and high cell density at an early stage of morphogenesis in N-acetyl-D-glucosamine medium. Nihon Ishinkin Gakkai Zasshi. 2007;48:159–67.

    Article  CAS  PubMed  Google Scholar 

  47. Han TL, Cannon RD, Villas-Bôas SG. The metabolic response of Candida albicans to farnesol under hyphae-inducing conditions. FEMS Yeast Res. 2012;12:879–89.

    Article  CAS  PubMed  Google Scholar 

  48. Deveau A, Hogan DA. Linking quorum sensing regulation and biofilm formation by Candida albicans. Methods Mol Biol. 2011;692:219–33.

    Article  CAS  PubMed  Google Scholar 

  49. Stagljar I, te Heesen S, Aebi M. New phenotype of mutations deficient in glucosylation of the lipid-linked oligosaccharide: cloning of the ALG8 locus. Proc Natl Acad Sci U S A. 1994;91:5977–81.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Rintala E, Pitkänen JP, Vehkomäki ML, Penttilä M, Ruohonen L. The ORF YNL274c (GOR1) codes for glyoxylate reductase in Saccharomyces cerevisiae. Yeast. 2007;24:129–36.

    Article  CAS  PubMed  Google Scholar 

  51. Ljungdahl PO, Daignan-Fornier B. Regulation of amino acid, nucleotide, and phosphate metabolism in Saccharomyces cerevisiae. Genetics. 2012;190:855–929.

    Article  Google Scholar 

  52. Peng B, Chen X, Shen Y, Bao X. [Effect of controlled overexpression of xylulokinase by different promoters on xylose metabolism in Saccharomyces cerevisiae]. Wei Sheng Wu Xue Bao. 2011;51:914–22.

    CAS  PubMed  Google Scholar 

  53. Sacksteder KA, Biery BJ, Morrell JC, Goodman BK, Geisbrecht B, Cox RP, et al. Identification of the α-aminoadipic semialdehyde synthase which is defective in familial hyperlysinemia. Am J Hum Genet. 2000;66:1736–43.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Pal S, Tiwari A, Sharma K, Sharma SK. Does conserved domain SOD1 mutation has any role in ALS severity and therapeutic outcome? BMC Neurosci. 2020;21:42.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Vattepu R, Klausmeyer RA, Ayella A, Yadav R, Dille JT, Saiz S, et al. Conserved tryptophan mutation disrupts structure and function of immunoglobulin domain revealing unusual tyrosine fluorescence. Protein Sci. 2020;29:2062–74.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Gromiha MM, Parry DAD. Characteristic features of amino acid residues in coiled-coil protein structures. Biophys Chem. 2004;111:95–103.

    Article  CAS  PubMed  Google Scholar 

  57. Zimin A, Marçais G, Puiu D, Roberts M, Salzberg SL, Yorke JA. The MaSuRCA genome assembler. Bioinformatics. 2013;29:2669–77.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. J.M. Palmer. Funannotate: Pipeline for Genome Annotation. 2016. (https://github.com/nextgenusfs/funannotate)

  59. Vincent AT, Schiettekatte O, Goarant C, Neela VK, Bernet E, Thibeaux R, et al. Revisiting the taxonomy and evolution of pathogenicity of the genus Leptospira through the prism of genomics. PLoS Negl Trop Dis. 2019;13:e0007270.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Deatherage DE, Barrick JE. Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq. Methods Mol Biol. 2014;1151:165–88.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Lu S, Wang J, Chitsaz F, Derbyshire MK, Geer RC, Gonzales NR et al. CDD/SPARCLE: The conserved domain database in 2020. Nucleic Acids Res. 2020;48:D265–8.

  62. McGuffin LJ, Bryson K, Jones DT. The PSIPRED protein structure prediction server. Bioinformatics. 2000;16:404–5.

    Article  CAS  PubMed  Google Scholar 

  63. Nugent T, Jones DT. Transmembrane protein topology prediction using support vector machines. BMC Bioinformatics. 2009;10:1–11.

    Article  Google Scholar 

  64. Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, et al. STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 2019;47:D607–13.

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

The authors would like to thank Cynthia Gagné-Thivierge (Université Laval) for her technical assistance.

Funding

This work was supported by the Natural Sciences and Engineering Research Council of Canada (NSERC) grants from A.T.V and S.J.C.

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Authors and Affiliations

  1. Département des sciences animales, Faculté des sciences de l’agriculture et de l’alimentation, Université Laval, Pavillon Paul-Comtois, 2425 rue de l’Agriculture, G1V 0A6, Quebec City, QC, Canada

    Sima Mohammadi & Antony T. Vincent

  2. Institut de biologie intégrative et des systèmes, Université Laval, Quebec City, QC, Canada

    Sima Mohammadi, Steve J. Charette & Antony T. Vincent

  3. Département de stomatologie, Faculté de Médecine Dentaire, Université de Montréal, Montreal City, QC, Canada

    Annie Leduc & Jean Barbeau

  4. Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec, Quebec City, QC, Canada

    Steve J. Charette

  5. Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Quebec City, QC, Canada

    Steve J. Charette

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  1. Sima Mohammadi
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  2. Annie Leduc
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Contributions

A.T.V, S.J.C and J.B. designed and supervised the project. S.M. and A.L. collected and generated the data, and performed analysis. S.M. and A.L. contributed to sample preparation. S.M. prepared the draft manuscript. All authors reviewed and revised the manuscript. The authors read and approved the final manuscript.

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Correspondence to Antony T. Vincent.

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Additional file 1. Figure S1.

The percentage of proteins with amino acid changes in every chromosome of the reference strain SC5314, with respect to the total number of proteins by chromosome.

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Mohammadi, S., Leduc, A., Charette, S.J. et al. Amino acid substitutions in specific proteins correlate with farnesol unresponsiveness in Candida albicans. BMC Genomics 24, 93 (2023). https://doi.org/10.1186/s12864-023-09174-y

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Keywords

  • Candida albicans
  • Farnesol
  • Amino acid substitutions
  • Genomics
  • Evolution

BMC Genomics

ISSN: 1471-2164

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