Open Access

Genome-wide screen for modifiers of Parkinson's disease genes in Drosophila

Molecular Brain20114:17

DOI: 10.1186/1756-6606-4-17

Received: 14 February 2011

Accepted: 19 April 2011

Published: 19 April 2011

Abstract

Background

Mutations in parkin and PTEN-induced kinase 1 (Pink1) lead to autosomal recessive forms of Parkinson's disease (PD). parkin and Pink1 encode a ubiquitin-protein ligase and a mitochondrially localized serine/threonine kinase, respectively. Recent studies have implicated Parkin and Pink1 in a common and evolutionarily conserved pathway for protecting mitochondrial integrity.

Results

To systematically identify novel components of the PD pathways, we generated a genetic background that allowed us to perform a genome-wide F1 screen for modifiers of Drosophila parkin (park) and Pink1 mutant phenotype. From screening ~80% of the fly genome, we identified a number of cytological regions that interact with park and/or Pink1. Among them, four cytological regions were selected for identifying corresponding PD-interacting genes. By analyzing smaller deficiency chromosomes, available transgenic RNAi lines, and P-element insertions, we identified five PD-interacting genes. Among them, opa1 and drp1 have been previously implicated in the PD pathways, whereas debra (dbr), Pi3K21B and β4GalNAcTA are novel PD-interacting genes.

Conclusions

We took an unbiased genetic approach to systematically isolate modifiers of PD genes in Drosophila. Further study of novel PD-interacting genes will shed new light on the function of PD genes and help in the development of new therapeutic strategies for treating Parkinson's disease.

Background

Parkinson's disease (PD) is the second most common neurodegenerative disease. It is characterized by the loss of nigral dopaminergic neurons. Mutations in Pink1 and Parkin cause autosomal recessive early-onset Parkinson's disease in humans [1, 2]. Together mutations in these genes account for greater than 50% of familial Parkinson disease (PD) and ~20% of early-onset sporadic cases [35]. Recent studies on characterizing the function of Parkin and Pink1 have significantly advanced our understanding of PD pathogenesis.

Parkin has E3-ubiquitin ligase activity, and is shown to degrade abnormally folded proteins [6]. For instance, Parkin ubiquitinates and degrades proteins such as CDCrel-1 [7], Parkin-associated endothelin receptor-like (Pael) receptor [8], α-synuclein [9], synphilin-1 [10], and cyclin E [11]. Thus, Parkin dysfunction in regulating the level of other proteins or itself through protein degradation may contribute to PD pathogenesis.

Pink1 is a mitochondria-localized serine/threonine kinase [2, 12, 13]. A recent study suggests that Pink1 directly phosphorylates Parkin [14]. In addition, Pink1 may directly or indirectly induce the phosphorylation of the HSP75 chaperone TRAP1 [12] and the mitochondrial protease HtrA2 [13].

Accumulated evidence supports that Pink1 and Parkin act together in a common and conserved pathway to protect mitochondrial integrity (for review, see [15]). For instance, it is reported that overexpression of Drosophila Parkin (park) could rescue mitochondrial defects caused by Pink1 mutations both in Drosophila [1619] and mammalian systems [20, 21]. Recent studies also indicate that Pink1-dependent recruitment of Park into mitochondria is required for the clearance of damaged mitochondria [2225].

Drosophila melanogaster has proven to be a powerful model system for understanding the function of PD genes. Several PD genes such as park, Pink1, LRRK2 and HtrA1 have orthologs in Drosophila. Interfering with their function caused PD-like phenotypes in Drosophila [1719, 2629]. Genetic studies in Drosophila have begun to reveal new targets for the development of new therapeutic approaches to treat PD. For instance, Pallanck and colleagues previously conducted a genetic screen to isolate modifiers of partial lethality caused by complete loss of park in Drosophila [30]. From ~1400 P-element insertions affecting less than 10% of the fly genome, they identified several genes that regulate oxidative stress and innate immune responses [30].

In this study, we conducted a systematic genetic screen to isolate park- and/or Pink1-interacting regions that cover ~80% of the entire fly genome. We generated a genetic background in which park or Pink1 was knocked down. The availability of this genetic tool allowed us to perform a F1 genetic screen to identify cytological regions on the 2nd and 3rd chromosome that interact with park and/or Pink1. We found that 31 cytological regions modify both park and Pink1 wing-posture phenotype. In addition, 21 cytological regions showed interactions with both Pink1 and park in adult lethality test. We then selected four cytological regions for fine mapping, which identified two known PD-interacting genes opa1 and drp1, and three novel PD-interacting genes debra, Pi3K21B and β4GalNAcTA.

Methods

Drosophila stocks

UAS-Pink1-RNAi, UAS-park RNAi and other transgenic RNAi lines were obtained from the VDRC stock center. A collection of deficiencies uncovering >92% of cytological regions on 2nd and 3rd chromosomes were obtained from the Bloomington Drosophila Stock Center. Smaller deficiencies and P-element insertions mapped within large PD-interacting cytological regions were also obtained from the Bloomington Drosophila Stock Center. Balancer stocks CyO,GAL80 and TM3,GAL80 were provided by D.van Meyel. The parkedpkΔ21/TM3,Sb line was provided by M. Guo (UCLA). Pink1B9/FM7,Act-GFP and park25/TM3,Sb stocks were provided by T. Fon. Df(2R)β4GalNAcTA[20.1] and β4GalNAcTA4.1 lines were obtained from N. Haines.

Genetics

To knock down Pink1 or park, tubulin-GAL4 (tub-GAL4) flies were crossed with UAS-Pink1-RNAi or UAS-park-RNAi flies to ubiquitously express Pink1-RNAi or park RNAi. Since fly stocks with ubiquitous expression of Pink1-RNAi or park RNAi under control of tub-GAL4 are not healthy, genetic crosses were performed to generate UAS-Pink1-RNAi/CyO,GAL80; tub-GAL4/TM3,Sb and UAS-park-RNAi;tub-Gal4/TM3,Sb,GAL80 stocks, in which GAL4 is inhibited by GAL80 to prevent the expression of UAS-Pink1-RNAi or UAS-park-RNAi in parental stocks [31].

F1 screen was performed by crossing individual deficiency lines from 2nd and 3rd chromosome deficiency kits with UAS-Pink1-RNAi/CyO,GAL80; tub-GAL4/TM3,Sb or UAS-park-RNAi;tub-Gal4/TM3,Sb,GAL80 flies. The F1 progeny in Pink1-RNAi background were reared at 25°, and the F1 progeny in park-RNAi background were kept at 29°. F1 progeny were collected for 4-6 days and separated according to their date of eclosion. The modification of wing-posture phenotype by each deficiency chromosome was scored on post-eclosion day 3 for Pink1 screen and on post-eclosion day 6 for park screen. Wing posture phenotype in both male and female F1 flies was scored, and the modifying effect on penetrance was determined by counting the percentage of both held-up-wing flies and drooped-wing flies. For park and Pink1 screen, 212 and 217 deficiencies in the deficiency kit were screened, respectively.

Selected deficiency lines were also crossed with Pink1B9/FM7,Act-GFP female flies. F1 progeny were scored for the modification of the wing-posture phenotype. The F1 progeny were also scored for adult lethality test.

Analysis of wing phenotype, longevity and fertility

For analysis of abnormal wing phenotype, ~20 flies were placed per vial. Flies with both wings held-up or drooped were counted.

For longevity test, flies were collected upon eclosion and transferred to new vials every 4-6 days. Mortality was scored daily. The assay was performed in triplicate. Survival curves were plotted using GraphPad software.

To test fertility of male flies, individual male flies were crossed with three (w1118) virgin females. After 10 days, the number of vials with progeny were counted.

Statistical Analysis

Student's t-test was used for statistical analysis.

Results

Characterization of park and Pink1 knockdown phenotypes

Previous studies show that loss of park or loss of Pink1 caused similar phenotypes, such as abnormal wing morphology, male sterility, reduced climbing ability, decreased longevity and loss of dopaminergic neurons [1719, 29]. To generate a "park-inhibited" or "Pink1- inhibited" background suitable for systematic F1 genetic screen, we used the GAL4-UAS system [32] to knock down the level of Pink1 or park in flies.

Consistent with previous reports [1719, 29], we found that ubiquitous knockdown of Pink1 or park by expressing UAS-park-RNAi or UAS-Pink1-RNAi transgenes under control of the tub-GAL4 driver, caused male sterility (compared to 100% fertility in wild-type control, Pink1 and park knockdown flies showed 14.3% and 44.4% fertility, respectively), reduced life span, and abnormal wing posture (i.e. held up or drooped) (Figure 1). Those phenotypes resembled that observed in park and Pink1 loss-of-function mutants [1719, 29].
https://static-content.springer.com/image/art%3A10.1186%2F1756-6606-4-17/MediaObjects/13041_2011_Article_115_Fig1_HTML.jpg
Figure 1

Knockdown of PD genes induces a wing position phenotype in adult flies. A-C, Ubiquitous knockdown of PD genes in flies induces an abnormal wing position phenotype (i.e. held up or drooped wing). A. Wild-type wing position in flies carrying only the tub-GAL4 driver. B, A park knockdown fly (i.e. a fly carrying both the tub-GAL4 driver and UAS-park-RNAi transgene). The "held-up" wing position phenotype was observed when UAS-park-RNAi was ubiquitously expressed under control of the tub-GAL4 driver. C, The "drooped" wing phenotype was observed in a Pink1 knockdown fly (i.e. a fly carrying both the tub-GAL4 driver and UAS-Pink1-RNAi transgene). D, Survival curves of park knockdown flies (solid line) and control flies (i.e. flies carrying only the UAS-park transgene) (dashed line). The experiments were performed at 25°C (green) and 29°C (red). Numbers in brackets represent sample numbers. Error bars represent SEM.

We then tested if the penetrance and severity of above phenotypes could be enhanced by increasing the expression level of the UAS-park-RNAi transgene. This was achieved by elevating temperature, which increases the activity of GAL4 leading to higher expression of UAS-transgenes [32]. Indeed, we found that increasing the expression level of park-RNAi significantly enhanced the phenotype. The penetrance of wing-posture phenotype in park knockdown flies was increased from ~2.1% at 25°C to ~22.4% at 29°C. The maximal life span of park knockdown flies was further reduced from ~67 days at 25°C to ~17 days at 29°C. The fertility of male park knockdown flies was also reduced from ~44.4% at 25°C to ~30% at 29°C.

We also examined the effect of increasing the level of Pink1-RNAi transgene on wing posture, male sterility and longevity. In Pink1 knockdown flies, the penetrance of wing-posture phenotype was increased from ~2.9% at room temperature to ~91% at 29°C. The maximal life span of Pink1 knockdown flies was reduced from ~55 days at room temperature to ~18 days at 29°C. The fertility of male Pink1 knockdown flies was also decreased from ~14.3% at room temperature to 0% at 29°C.

F1 screen for modifiers of the park knockdown phenotype

To identify novel modifiers of the PD pathway, we set out to conduct a systematic screen to identify cytological regions on the 2nd and 3rd chromosome that interact with park (Figure 2).
https://static-content.springer.com/image/art%3A10.1186%2F1756-6606-4-17/MediaObjects/13041_2011_Article_115_Fig2_HTML.jpg
Figure 2

A genetic scheme for isolating modifiers of Parkinson's disease genes in Drosophila. Deficiencies (Df) from the Bloomington deficiency kits were crossed individually into the park or Pink1 knockdown mutant background. F1 progeny were scored for potential phenotypic enhancement (i.e. an increase in the penetrance of the wing phenotype) or suppression (i.e. a decrease in the penetrance of the wing phenotype). Abbreviations: En, enhancement; Su, suppression; tub-GAL4, tubulin-GAL4.

Prior to the screen, we examined if the park knockdown mutant background is sensitive to the reduction in the dosage of known genes in the pathway. We found that reducing the level of endogenous park substantially increased the penetrance of the park-RNAi-induced wing posture phenotype from ~15% (n = 76) (genotype: park RNAi; +/+) to ~43% (n = 97) (genotype: park RNAi; park25/+) (P < 0.05). Since Pink1 and park have previously been shown to act in a common pathway [1719], we also tested if the park knockdown background is sensitive to a reduction in the level of Pink1. Indeed, we found that Pink1 heterozygostiy significantly enhanced the penetrance of the park-RNAi-induced wing posture phenotype from ~13% (n = 90) (genotype: +/+; park RNAi) to ~40% (n = 32) (genotype: Pink1 B9 /+; park RNAi) (P < 0.01).

To systematically identify modifiers of this park wing-posture phenotype, we crossed a large collection of deficiencies on the 2nd and 3rd chromosome into the park knockdown mutant background. In each deficiency chromosome, a portion of cytological regions was deleted. Thus, crossing a deficiency chromosome into the park knockdown background led to 50% reduction in the dosage of genes located within the deleted cytological region.

From this screen, we identified 26 cytological regions that enhanced the park wing-posture phenotype (Table 1), and 53 cytological regions that suppressed the wing-posture phenotype (Table 2). We also found that reducing the dosage of genes by 50% in 48 cytological regions in park knockdown flies caused lethality prior to the adult stage (Table 3). No such adult lethality was observed when park was knocked down alone, or the dosage of those 48 cytological regions was reduced by 50% in wild type background.
Table 1

Enhancers of the park-RNAi wing phenotype

Deficiencies

Breakpoints

Strength of modificationa

Df(2L)net-PMF

21A1;21B7-8

++

Df(2L)BSC28

23C5-D1;23E2

++++

Df(2L)cl-h3

25D2-4;26B2-5

++

Df(2L)BSC7

26D10-E1;27C1

++

Df(2L)ED611

29B4;29C3

++

Df(2L)BSC17

30C3-5;30F1

++

Df(2L)Mdh

30D-30F;31F

+++++

Df(2L)BSC50

30F5;31B1

++++++

Df(2L)FCK-20

32D1;32F1-3

+++

Df(2R)nap9

42A1-2;42E6-F1

+++++

Df(2R)cn9

42E;44C

++

Df(2R)H3E1

44D1-4;44F12

+++

Df(2R)en30

48A3-4;48C6-8

+++

Df(2R)BSC39

48C5-D1;48D5-E1

++++

Df(2R)BSC161

54B2;54B17

++++

Df(2R)Exel7162

56F11;56F16

++++

Df(2R)59AD

59A1-3;59D1-4

+++

Df(3L)AC1

67A2;67D11-13

+++++

Df(3L)XS533

76B4;77B

++

Df(3L)BSC249

79B2;79D2

++

Df(3R)BSC47

83B7-C1;83C6-D1

++

Df(3R)Tpl10

83C1-2;84B1-2

++

Df(3R)BSC43

92F7-93A1;93B3-6

++

Df(3R)BSC56

94E1-2;94F1-2

++

Df(3R)BSC137

95A2-4;95A8-B1

+++

Df(3R)BSC42

98B1-2;98B3-5

++

Each deficiency was crossed into the park RNA i background and the wing posture phenotype was scored. Crosses were maintained at 29°C.

a Each '+' represents 1.0 SD from the mean pentrance (i.e. ~22.4%) observed for park RNAi alone flies.

Table 2

Suppressors of the park-RNAi wing phenotype

Deficiencies

Breakpoints

Strength of modificationa

Df(2L)BSC106

21B7;21C2

++++

Df(2L)dp-79b

22A2-3;22D5-E1

++++

Df(2L)ed1

24A2;24D4

++++

Df(2L)sc19-8

24C2-8;25C8-9

++

Df(2L)BSC110

25C1;25C4

++

Df(2L)BSC109

25C4;25C8

++++

Df(2L)E110

25F3-26A1;26D3-11

++

Df(2L)BSC142

28C3;28D3

++++

Df(2L)BSC143

31B1;31D9

++

Df(2L)BSC145

32C1;32C1

+++

Df(2L)b87e25

34B12-C1;35B10-C1

++++

Df(2L)C'

h35;h38L

++

Df(2R)BSC3

48E12-F4;49A11-B6

++++

Df(2R)Exel7131

50E4;50F6

++++

Df(2R)BSC550

53C1;53C6

++

Df(2R)robl-c

54B17-C4;54C1-4

++

Df(2R)BSC45

54C8-D1;54E2-7

++++

Df(2R)P34

55E2-4;56C1-11

++++

Df(2R)AA21

56F9-17;57D11-12

++

Df(2R)BSC155

60B9;60C4

+++

Df(2R)M60E

60E2-3;60E11-12

++

Df(3L)Aprt-1

62A10-B1;62D2-5

++++

Df(3L)BSC181

62A11;62B7

++++

Df(3L)XDI98

65A2;65E1

++

Df(3L)BSC33

65E10-F1;65F2-6

++

Df(3L)pbl-X1

65F3;66B10

++++

Df(3L)66C-G28

66B8-9;66C9-10

+++

Df(3L)h-i22

66D10-11;66E1-2

+++

Df(3L)Scf-R6

66E1-6;66F1-6

++

Df(3L)BSC283

67C7;67D5

+++

Df(3L)eyg[C1]

69A4-5;69D4-6

++++

Df(3L)BSC10

69D4-5;69F5-7

++++

Df(3L)BSC12

69F6-70A1;70A1-2

++

Df(3L)fz-GF3b

70C1-2;70D4-5

+++

Df(3L)XG5

71C2-3;72B1-C1

++

Df(3L)fz2

75F10-11;76A1-5

++++

Df(3L)ME107

77F3;78C8-9

+++

Df(3R)ME15

81F3-6;82F5-7

++

Df(3R)3-4

82F3-4;82F10-11

++++

Df(3R)p-XT103

85A2;85C1-2

++++

Df(3R)BSC38

85F1-2;86C7-8

++

Df(3R)sbd105

88F9-89A1;89B9-10

++

Df(3R)sbd104

89B5;89C2-7

++

Df(3R)P115

89B7-8;89E7

+++

Df(3R)Exel9012

94E9;94E13

+++

Df(3R)Exel6195

95A4;95B1

++

Df(3R)Exel9014

95B1;95D1

+++

Df(3R)Exel6196

95C12;95D8

+++

Df(3R)crb-F89-4

95D7-D11;95F15

+++

Df(3R)slo8

96A2-7;96D2-4

++++

Df(3R)Exel6202

96C9;96E2

+++

Df(3R)Exel6203

96E2;96E6

++++

Df(3R)B81

99D3;3Rt

++++

a Each '+' represents 0.5 SD from the mean (~22.4%) observed for park RNAi alone flies.

Table 3

List of deficiencies showing lethal interactions with park knockdown

Deficiencies

Breakpoints

Df(2L)BSC16

21C3-4;21C6-8

Df(2L)ast2

21D1-2;22B2-3

Df(2L)BSC37

22D2-3;22F1-2

Df(2L)dpp[d14]

22E4-F2;22F3-23A1

Df(2L)C144

22F4-23A1;23C2-4

Df(2L)Exel6011

25C8;25D5

Df(2L)N22-14

29C1-2;30C8-9

Df(2L)J2

31B;32A

Df(2L)cact-255rv64

35F-36A;36D

Df(2L)TW137

36C2-4;37B9-C1

In(2R)bw[VDe2L]Cy[R]

h42-h43;42A2-3

Df(2R)Np5

44F10;45D9-E1

Df(2R)BSC29

45D3-4;45F2-6

Df(2R)X1

46C;47A1

Df(2R)en-A

47D3;48B2

Df(2R)vg-C

49A4-13;49E7-F1

Df(2R)CX1

49C1-4;50C23-D2

Df(2R)BSC18

50D1;50D2-7

Df(2R)Exel7130

50D4;50E4

Df(2R)Jp1

51D3-8;52F5-9

Df(2R)BSC49

53D9-E1;54B5-10

Df(2R)PC4

55A;55F

Df(2R)Egfr5

57D2-8;58D1

Df(2R)ED4065

60C8;60E8

Df(2R)Kr10

60F1;60F5

Df(3L)M21

62F;63D

Df(3L)HR119

63C2;63F7

Df(3L)GN34

63E6-9;64A8-9

Df(3L)ZN47

64C;65C

Df(3L)vin5

68A2-3;69A1-3

Df(3L)st-f13

72C1-D1;73A3-4

Df(3L)81k19

73A3;74F

Df(3L)W10

75A6-7;75C1-2

Df(3L)ED4978

78D5;79A2

Df(3L)BSC223

79A3;79B3

Df(3R)Exel6144

83A6;83B6

Df(3R)WIN11

83E1-2;84A5

Df(3R)p712

84D4-6;85B6

Df(3R)M-Kx1

86C1;87B1-5

Df(3R)T-32

86E2-4;87C6-7

Df(3R)ry615

87B11-13;87E8-11

Df(3R)ea

88E7-13;89A1

Df(3R)DG2

89E1-F4;91B1-B2

Df(3R)Dl-BX12

91F1-2;92D3-6

Df(3R)e-R1

93B6-7;93D2

Df(3R)Exel6197

95D8;95E5

Df(3R)Espl3

96F1;97B1

Df(3R)IR16

97F1-2;98A

Df(2L)BSC16

21C3-4;21C6-8

Df(2L)ast2

21D1-2;22B2-3

Df(2L)BSC37

22D2-3;22F1-2

Above deficiencies, when crossed into the park knockdown background, significantly reduced the viability of park knockdown flies (less than five flies eclosed).

F1 screen for modifiers of the Pink1 knockdown phenotype

Above deficiencies were also screened using the Pink1 knockdown mutant background. Pink1 knockdown mutant flies displayed the wing-posture phenotype at the penetrance of ~64% (n = 314) at 25°C. Among 26 enhancer-containing cytological regions identified from the Park screen (Table 1), 8 cytological regions, when reduced by 50% in dosage, also enhanced the penetrance of the Pink1 knockdown wing phenotype (Table 4). This screen also identified 9 enhancer-containing cytological regions that were not uncovered from the park screen (Table 4). Among 53 suppressor-containing cytological regions identified from the park screen (Table 2), we found that 23 cytological regions also contained suppressors of the Pink1 wing-posture phenotype (Table 5). In addition, we found that 30 cytological regions, when reduced by 50% in dosage, suppressed the Pink1 wing phenotype but not the park wing phenotype (Table 5).
Table 4

Enhancers of the Pink1-RNAi wing phenotype

Deficiencies

Breakpoints

Strength of modificationa

Df(2L)net-PMF

21A1;21B7-8

++

Df(2L)BSC4

21B7-C1;21C2-3

++

Df(2L)BSC16

21C3-4;21C6-8

++

Df(2L)BSC17

30C3-5;30F1

++

Df(2L)BSC50

30F5;31B1

+++

Df(2R)nap9

42A1-2;42E6-F1

++

Df(2R)cn9

42E;44C

++

Df(2R)BSC29

45D3-4;45F2-6

++

Df(2R)BSC39

48C5-D1;48D5-E1

++

Df(2R)BSC3

48E12-F4;49A11-B6

+++

Df(2R)BSC22

56D7-E3;56F9-12

++

Df(3L)BSC27

65D4-5;65E4-6

++

Df(3L)BSC14

67E3-7;68A2-6

+++

Df(3L)XG5

71C2-3;72B1-C1

+++

Df(3L)ED4782

75F2;76A1

++

Df(3L)HD1

79D3-E1;79F3-6

++

Df(3R)BSC47

83B7-C1;83C6-D1

++

Df(3R)Tpl10

83C1-2;84B1-2

++

Each deficiency was crossed into the Pink1 knockdown background and the wing posture phenotype was scored. Crosses were maintained at 25°C.

a Each '+' represents 1.0 SD from the mean (i.e. ~64.5%) observed for Pink1 RNAi alone flies. Deficiencies that also enhanced park RNAi wing posture phenotype (Table 1) are indicated in bold.

Table 5

Suppressors of the Pink1-RNAi wing phenotype

Deficiencies

Breakpoints

Strength of modificationa

Df(2L)BSC106

21B7;21C2

+++

Df(2L)dp-79b

22A2-3;22D5-E1

+++++

Df(2L)JS17

23C1-2;23E1-2

+++

Df(2L)drm-P2

23F3-4;24A1-2

+++

Df(2L)ed1

24A2;24D4

+++

Df(2L)BSC109

25C4;25C8

++++

Df(2L)E110

25F3-26A1;26D3-11

++++

Df(2L)BSC6

26D3-E1;26F4-7

++++

Df(2L)Dwee1-W05

27C2-3;27C4-5

+++

Df(2L)XE-3801

27E2;28D1

+++

Df(2L)BSC142

28C3;28D3

++++

Df(2L)BSC143

31B1;31D9

+++

Df(2L)BSC32

32A1-2;32C5-D1

+++++

Df(2L)BSC147

34C1;34C6

++++

Df(2L)Exel6049

40A5;40D3

+++

Df(2R)w45-30n

45A6-7;45E2-3

++++

Df(2R)CB21

48E;49A

+++

Df(2R)Exel7130

50D4;50E4

++++

Df(2R)Exel7131

50E4;50F6

+++++

Df(2R)BSC11

50E6-F1;51E2-4

+++

Df(2R)BSC550

53C1;53C6

++++

Df(2R)robl-c

54B17-C4;54C1-4

+++

Df(2R)k10408

54C1-4;54C1-4

+++

Df(2R)P34

55E2-4;56C1-11

++++

Df(2R)Exel7162

56F11;56F16

+++

Df(2R)or-BR6

59D5-10;60B3-8

+++

Df(3L)M21

62F;63D

+++

Df(3L)GN34

63E6-9;64A8-9

+++

Df(3L)XDI98

65A2;65E1

+++

Df(3L)BSC33

65E10-F1;65F2-6

+++

Df(3L)66C-G28

66B8-9;66C9-10

+++

Df(3L)BSC13

66B12-C1;66D2-4

+++

Df(3L)Scf-R6

66E1-6;66F1-6

+++++

Df(3L)BSC10

69D4-5;69F5-7

+++

Df(3L)st-f13

72C1-D1;73A3-4

++++

Df(3L)81k19

73A3;74F

+++++

Df(3L)kto2

76B1-2;76D5

+++

Df(3L)ri-79c

77B-C;77F-78A

++++

Df(3L)ri-XT1

77E2-4;78A2-4

++++

Df(3L)ME107

77F3;78C8-9

+++

Df(3L)BSC249

79B2;79D2

++++

Df(3R)p-XT103

85A2;85C1-2

+++++

Df(3R)M-Kx1

86C1;87B1-5

++++

Df(3R)ea

88E7-13;89A1

+++

Df(3R)sbd104

89B5;89C2-7

+++

Df(3R)P115

89B7-8;89E7

++++

Df(3R)23D1

94A3-4;94D1-4

+++

Df(3R)crb-F89-4

95D7-D11;95F15

+++

Df(3R)Exel6197

95D8;95E5

+++

Df(3R)Exel6202

96C9;96E2

+++

Df(3R)Exel6203

96E2;96E6

++++

Df(3R)Tl-P

97A;98A1-2

+++

Df(3R)IR16

97F1-2;98A

+++++

a Each '+' represents 1.0 SD from the mean (i.e. ~64.5%) observed for Pink1 RNAi alone flies. Deficiencies that also suppressed the park RNAi wing posture phenotype (Table 2) are indicated in bold.

Among 50 cytological regions that caused adult lethality when their dosage was reduced by 50% in park knockdown background (Table 3), 21 cytological regions also displayed a similar lethal interaction with Pink1 knockdown (Table 6). Five cytological regions only showed lethal interactions with Pink1 but not park (Table 6).
Table 6

List of deficiencies showing lethal interactions with Pink1 knockdown

Deficiencies

Breakpoints

Df(2L)BSC37

22D2-3;22F1-2

Df(2L)dpp[d14]

22E4-F2;22F3-23A1

Df(2L)C144

22F4-23A1;23C2-4

Df(2L)sc19-8

24C2-8;25C8-9

Df(2L)Exel6011

25C8;25D5

Df(2L)b87e25

34B12-C1;35B10-C1

Df(2L)TW137

36C2-4;37B9-C1

In(2R)bw[VDe2L]Cy[R]

h42-h43;42A2-3

Df(2R)M41A4

41A;41A

Df(2R)X1

46C;47A1

Df(2R)CX1

49C1-4;50C23-D2

Df(2R)BSC49

53D9-E1;54B5-10

Df(2R)ED4065

60C8;60E8

Df(2R)Kr10

60F1;60F5

Df(3L)HR119

63C2;63F7

Df(3L)vin5

68A2-3;69A1-3

Df(3L)vin7

68C8-11;69B4-5

Df(3L)W10

75A6-7;75C1-2

Df(3L)ED4978

78D5;79A2

Df(3L)BSC223

79A3;79B3

Df(3R)Exel6144

83A6;83B6

Df(3R)p712

84D4-6;85B6

Df(3R)T-32

86E2-4;87C6-7

Df(3R)DG2

89E1-F4;91B1-B2

Df(3R)Dl-BX12

91F1-2;92D3-6

Df(3R)B81

99D3;3Rt

Above deficiencies, when crossed into the Pink1 knockdown background, significantly reduced the viability of Pink1 knockdown flies (less than five flies eclosed). Deficiencies that display a similar lethal interaction with park knockdown (Table 3) are indicated in bold.

Analysis of genetic interactions using a Pink1 null mutant allele

Cytological regions identified from above RNAi-based screen may contain genes that function in the Pink1/park pathway, or genes that function in a parallel pathway that act together with the Pink1/park pathway to regulate mitochondrial function. To further characterize these cytological regions, we performed genetic analysis using a Pink1 null mutant allele to test the potential interactions between Pink1 and cytological regions that interact with both Pink1 and park in the above RNAi-based screen. Among six enhancer-containing cytological regions examined, five cytological regions, when reduced by 50% in dosage, also enhanced the wing phenotype in Pink1 null mutants (Table 7). Among 17 suppressor-containing cytological regions examined, 10 cytological regions, when reduced by 50% in dosage, also suppressed the wing phenotype in Pink1 null mutants (Table 7). Among 19 examined cytological regions that showed lethal interactions with both Pink1 and park in RNAi-based screens, 5 cytological regions, when reduced by 50% in dosage, also displayed the lethal phenotype in Pink1 null mutants (Table 8).
Table 7

Analysis of the interaction between a Pink1 null mutation and cytological regions that modified both park-RNAi and pink1-RNAi wing phenotype

  

Effects of modification

Deficiencies

Breakpoints

Pink1-RNAi

park-RNAi

Pink1 B9

Enhancers

    

Df(2L)net-PMF

21A1;21B7-8

++

++

n/d

Df(2L)BSC17

30C3-5;30F1

++

++

n/d

Df(2L)BSC50

30F5;31B1

+++

++++++

En

Df(2R)nap9

42A1-2;42E6-F1

++

+++++

En

Df(2R)cn9

42E;44C

++

++

En

Df(2R)BSC39

48C5-D1;48D5-E1

++

++++

En

Df(3R)BSC47

83B7-C1;83C6-D1

++

++

En

Df(3R)Tpl10

83C1-2;84B1-2

++

++

No

Suppressors

    

Df(2L)BSC106

21B7;21C2

---

----

Su

Df(2L)dp-79b

22A2-3;22D5-E1

-----

----

No

Df(2L)ed1

24A2;24D4

---

----

n/d

Df(2L)BSC109

25C4;25C8

----

----

Su

Df(2L)E110

25F3-26A1;26D3-11

----

--

n/d

Df(2L)BSC142

28C3;28D3

----

----

Su

Df(2L)BSC143

31B1;31D9

---

--

No

Df(2R)Exel7131

50E4;50F6

-----

----

Su

Df(2R)BSC550

53C1;53C6

----

--

No

Df(2R)robl-c

54B17-C4;54C1-4

---

--

n/d

Df(2R)P34

55E2-4;56C1-11

----

----

Su

Df(3L)XDI98

65A2;65E1

---

--

n/d

Df(3L)BSC33

65E10-F1;65F2-6

---

--

n/d

Df(3L)66C-G28

66B8-9;66C9-10

---

---

No

Df(3L)Scf-R6

66E1-6;66F1-6

-----

--

Su

Df(3L)BSC10

69D4-5;69F5-7

---

----

Su

Df(3L)ME107

77F3;78C8-9

---

---

No

Df(3R)p-XT103

85A2;85C1-2

-----

----

Su

Df(3R)sbd104

89B5;89C2-7

---

--

n/d

Df(3R)P115

89B7-8;89E7

----

---

Su

Df(3R)crb-F89-4

95D7-D11;95F15

---

---

No

Df(3R)Exel6202

96C9;96E2

---

---

No

Df(3R)Exel6203

96E2;96E6

----

----

Su

Abbreviations: n/d, not determined; Su, suppression; En, enhancement; No, no modification.

Table 8

Analysis of the interaction between a Pink1 null allele and deficiencies that exhibited lethal interactions with both park and Pink1 knockdown

Deficiencies

Breakpoints

Synthetic lethal with pink1B9

Df(2L)BSC37

22D2-3; 22F1-2

No

Df(2L)dpp[d14]

22E4-F2; 22F3-23A1

Yes

Df(2L)C144

22F4-23A1; 23C2-4

Partial

Df(2L)Exel6011

25C8; 25D5

No

Df(2L)TW137

36C2-4; 37B9-C1

No

In(2R)bw[VDe2L]Cy[R]

h42-h43;42A2-3

Yes

Df(2R)M41A4

h44;42A2

Yes

Df(2R)X1

46C;47A1

n/d

Df(2R)CX1

49C1-4;50C23-D2

Yes

Df(2R)BSC49

53D9-E1;54B5-10

No

Df(2R)ED4065

60C8;60E8

 

Df(2R)Kr10

60F1;60F5

No

Df(3L)HR119

63C2;63F7

No

Df(3L)vin5

68A2-3;69A1-3

No

Df(3L)vin7

68C8-11;69B4-5

No

Df(3L)W10

75A6-7;75C1-2

No

Df(3L)ED4978

78D5;79A2

No

Df(3L)BSC223

79A3;79B3

No

Df(3R)Exel6144

83A6;83B6

No

Df(3R)p712

84D4-6;85B6

n/d

Df(3R)T-32

86E2-4;87C6-7

No

Df(3R)Dl-BX12

91F1-2;92D3-6

No

Molecular characterization of the PD-interacting cytological region 21A1-21B7

The PD-interacting cytological regions identified from above screens are relative large and contain a number of genes. As a first step towards molecular characterization of these PD-interacting cytological regions, we performed fine mapping in four selected PD-interacting cytological regions to identify corresponding PD-interacting genes. Those cytological regions were selected since they displayed strongest interactions with both park and Pink1.

From above screens, we found that reducing the dosage of the cytological region 21A1-21B7-8, deleted in the deficiency chromosome Df(2L) net-PMF, enhanced both park and Pink1 wing phenotype (Table 1 and 4). To identify the corresponding PD-interacting gene within this cytological region, we tested additional deficiency lines that carry smaller deletions within this region. We found that similar enhancement was observed when a smaller deficiency chromosome Df(2L)ED5878 was crossed into park or Pink1 knockdown background (Figure 3). Twenty two genes are disrupted in this deficiency chromosome, including dbr, galectin, CG11374, net, CG11376, Sam-S, CG4822, Gs1, CG31976, CG3709, CG11377, CG13694, CG31975, CG11455, Nhe1, CG3164, CG31974, CG3436, CG11454, CG33635, CG42399 and spen. Interestingly, we found that another smaller deficiency Df(2L) ED2809 in which only the debra (dbr) gene is deleted, also enhanced the park knockdown phenotype (~50% increase in penetrance compared to park RNAi alone, n = 104). Taken together, these results suggest strongly that dbr is largely, if not entirely, responsible for the observed interaction with PD genes.
https://static-content.springer.com/image/art%3A10.1186%2F1756-6606-4-17/MediaObjects/13041_2011_Article_115_Fig3_HTML.jpg
Figure 3

Molecular characterization of the PD-interacting cytological region 21A1-21B7. Genes (arrows) are listed according to their genomic location. The regions uncovered by the deficiencies used in the experiments are indicated (dashed lines). The effect of each deficiency is indicated as enhancement (+) or no enhancement (-).

Molecular characterization of two PD suppressor-containing cytological regions 21B7-21C2 and 50E4-50F6

Reducing the dosage of the cytological region 21B7-21C2, uncovered by the deficiency chromosome Df(2L)BSC106, suppressed both park and Pink1 wing phenotype (Table 2 and 5). From a collection of smaller deficiencies mapped within this region, we identified two overlapping deficiencies Df(2L)BSC454 and Df(2L)Pi3K21B, which like Df(2L)BSC106, both suppressed park and Pink1 wing phenotype (Figure 4A). The cytological region deleted in both Df(2L)BSC454 and Df(2L)Pi3K21B, contains four genes Hop, Pi3K21B, Plc21C and U2af38.
https://static-content.springer.com/image/art%3A10.1186%2F1756-6606-4-17/MediaObjects/13041_2011_Article_115_Fig4_HTML.jpg
Figure 4

Molecular characterization of two PD suppressor-containing cytological regions 21B7-21C2 and 50E4-50F6. A, Characterization of the PD-interacting cytological region 21B7-21C2. B, Characterization of the PD-interacting cytological region 50E4-50F6. The regions uncovered by the deficiencies used in the experiments are indicated (dashed line). The effect of each deficiency is indicated as suppression (+) or no suppression (-). The genes (arrows) are listed according to their genomic location. opa1EY09863 is an opal loss-of-function allele in which a P-element-containing sequence is inserted into the opa1 locus. Df(2R)β4GalNAcTA[20.1] and β4GalNAcTA4.1 were generated by imprecise excision [47]. In the Df(2R)β4GalNAcTA[20.1] allele, both β4GalNAcTA and CG8531 are deleted, while 610 base-pair sequence in the β4GalNAcTA gene is deleted in the β4GalNAcTA4.1 allele.

To further narrow down the PD-interacting gene within this region, we tested if any of above four genes interacts with PD genes. Among them, we found that knockdown the expression of Pi3K21B also significantly suppressed the Pink1 wing phenotype (~48% decrease in penetrance compared to Pink1 RNAi alone, n = 42). This result suggests that Pi3K21B is the corresponding PD-interacting gene.

Reducing the dosage of the cytological region 50E4-50F6, uncovered by the deficiency chromosome Df(2R)Exel7131, also suppressed both park and Pink1 knockdown wing phenotype (Table 2 and 5). However, another deficiency Df(2R)BSC700, in which the deleted cytological region partially overlaps with that affected in Df(2R)Exel7131, did not interact with park or Pink1. The cytological region deleted in Df(2R)Exel7131, but not in Df(2R)BSC700, carry nine genes (i.e. opa1-like, CG8485, CG8494, CG8503, Mdr50, Hsc70-5, CG8531, β4GalNAcTA and CG8547) (Figure 4B).

To test if the above genes interact with park or Pink1, we crossed available mutations into park or Pink1 knockdown background. We found that opa1 and β4GalNAcTA interact genetically with PD genes (Figure 4B). A heterozygous mutation of opa1 (i.e. opa1EY09863) significantly suppressed the park wing phenotype (~95% reduction in penetrance compared to park knockdown alone, n = 83). And heterozygous mutations of β4GalNAcTA, Df (2R)β4GalNAcTA[20.1] (deleting both β4GalNAcTA and its neighboring gene CG8547) and β4GalNAcTA4.1 (deleting part of the β4GalNAcTA gene only), significantly suppressed the Pink1 wing phenotype (for Df (2R)β4GalNAcTA[20.1], ~92% reduction in penetrance compared to Pink1 knockdown alone, n = 62; for β4GalNAcTA4.1, ~82% reduction in penetrance compared to Pink1 knockdown alone, n = 59).

drp1 is the corresponding gene of the cytological region 22F4-23A3 that displayed lethal interaction with PD genes

Two deficiencies, Df(2L)dpp[d14] (22E4-F2;22F3-23A1) and Df(2L)C144 (22F4-23A1;23C2-4), caused lethality when heterozygous in park RNAi, Pink1 RNAi or Pink1 null mutant background (Table 8). A smaller deficiency (i.e. Df(2L)ED136), which deletes the overlapping region defined by the above deficiencies, also caused partial lethality in the Pink1 null background (i.e. ~50% reduction in viability compared to controls). The cytological region deleted in Df(2L)ED136 contains 29 genes, of which mutations in drp1 have been previously implicated as an enhancer of park and Pink1 mutant phenotypes [16, 33, 34]. Hence, we used a mutant allele for drp1 (i.e. drp 1KG03815) to examine the potential interaction. Consistent with previous reports, we found that drp1 heterozygosity substantially enhanced the lethal phenotype in the Pink1 null background (i.e. ~82.8% reduction in viability compared to controls). This result strongly suggests that drp1 is the corresponding gene within the cytological region 22F4-23A3 that displayed lethal interaction with PD genes.

Discussion

In this study, we performed a genome-wide screen to isolate modifiers of PD genes. From this screen, we identified a number of cytological regions that interact with park and/or Pink1. Fine mapping of selected PD-interacting cytological regions led to the identification of corresponding PD-interacting genes. Among them, opa1 and drp1 have previously been implicated in Pink1/park-mediated mitochondrial quality control pathways. In addition, we also identified debra, Pi3K21B, and β4GalNAcTA as novel PD-interacting genes.

While several previous studies suggest that park and Pink1 function in a common pathway to regulate mitochondrial function, cytological regions identified from our park- and Pink1-modifying screens do not completely overlap. For instance, among cytological regions showing lethal interactions with Pink1, about 81% displayed similar interactions with park (Table 6). Among cytological regions modifying Pink1 wing phenotype, only ~44% showed similar interactions with park (Table 4 and 5). One possible explanation is that park and Pink1 knockdown genetic background have different sensitivity, which may account for the difference in their interactions with some cytological regions. Alternatively or additionally, the molecular network involving Park and Pink1 may be more complex than a simplified linear pathway.

A previous study by Pallanck and colleagues screened a collection of P-element insertions (covering less than 10% of the fly genome) that modify the partial lethality of park null mutants [30]. However, since their screen was conducted in homozygous park null mutant background, less than 10% of the fly genome was covered. To increase the coverage, we developed an RNAi-based strategy, which allowed us to perform a F1 screen that covered >80% of the fly genome. Several PD-interacting genes identified by Pallanck and colleagues in their previous screen [30], are located within PD-interacting cytological regions identified from our screen. For instance, Glutathione S-transferase 1 (Gst1) and Thioredoxin-2 (Trx-2) are located in PD-interacting cytological regions uncovered by Df(2R)BSC49 (Table 6) and Df(2L)N22-14 (Table 3), respectively.

While our screen using deficiencies greatly increases the coverage of genomic regions, there are several limitations. For instance, since cytological regions deleted in deficiency chromosomes contain a large number of genes (average ~50), it is possible that a cytological region containing PD-interacting genes may not be identified from our screen if both enhancers and suppressors are located within the same region. Similarly, this may also make it difficult to identify the corresponding genes, especially if the strong modifying effect is due to the presence of multiple weak modifiers within the same region. Additionally, since those deficiency chromosomes used in our screen may carry second-site mutations contributing to the observed interactions, it is necessary to characterize independent point mutations and/or deletions mapped within the same region.

Our screen isolated two known PD-interacting genes drp1 and Opa1. drp1 encodes a GTPase (i.e. the dynamin-related protein 1) that has been previously implicated in regulating mitochondrial fission [35], while opa1 (optic atrophy 1) encodes for another dynamin-related GTPase that promotes mitochondrial fusion [36, 37]. Consistent with previous reports [16, 33, 34], we showed that drp1 heterozygosity induced lethality prior to the adult stage in park or Pink1 knockdown background. We also showed that opa1 heterozygosity significantly suppressed the park-RNAi-induced wing phenotype. Similarly, previous reports showed that heterozygous mutations of opa1 suppressed indirect flight muscle degeneration and mitochondrial morphological phenotypes in Pink1 and park mutants [33, 34]. Together, these observations underscore the importance of PD-interacting genes in mitochondrial fission and fusion to facilitate mitochondrial quality control.

Among the three novel PD-interacting genes (i.e. debra, Pi3K21B, and β4GalNAcTA) isolated from our screen, debra (de terminer of br eaking down of Ci a ctivator) (dbr) heterozygosity led to strong enhancement of the park-RNAi- induced wing phenotype. dbr encodes a novel zinc-binding protein of 1007 amino-acid residues [38]. Cell culture studies showed that Dbr forms a complex with Slimb, a component of the SCF (Skpl, Cdc53 and F box) ubiquitin ligase complex, to mediate the polyubiquitination of the transcription factor Cubitus interruptus (Ci) and thus targets Ci into the lysosome for degradation [38]. This raises the interesting possibility that Dbr functions together with Park in the ubiquitin-proteasome pathway for the control of protein quality. Reducing the dosage of dbr may thus increase the accumulation of toxic protein substrates, leading to the enhancement of the park phenotype. In this context, it is worth noting that a recent study showed that reducing the level of dbr also enhanced Ataxin3- induced neurodegeneration in Drosophila, which also resulted from accumulation of pathogenic proteins [39]. Additionally, since Dbr is a zinc-binding protein, Dbr may also play a role in regulating the level of intracellular zinc. Zinc dyshomeostasis has been shown to cause abnormalities in autophagy that are associated with Alzheimer's disease, Parkinson's disease, and Huntington's disease [40]. Thus, it is possible that in addition to its interaction with Park in the ubiquitin-proteasome pathway, Dbr may interact with the PD pathway by regulating autophagy.

Another novel-PD-interacting gene Pi3K21B, identified in our screen as a suppressor of PD wing phenotype, encodes an SH2 domain-containing adaptor protein that binds to the Drosophila class IA Phosphoinisitide 3 Kinase (PI3K), Pi3K92E/Dp110 [41]. It has been shown that class IA PI3-kinases are activated by nutrient-responsive insulin signalling to regulate cell growth and proliferation [42]. Loss of Pi3K21B-binding sites completely abrogates the activation of Dp110 by the insulin receptor, which decreased cell growth leading to reduced body size [43]. One possible explanation for the observed interaction between Pi3K21B and PD genes is that reducing the level of Pi3K21B may decrease insulin signaling and metabolic activities. This may be achieved by reducing the level of the TOR (target of rapamycin) signaling pathway. TOR can be activated by the PI3K/Akt pathway to regulate cell growth and metabolism (for review, see [44]). Recent studies show that reducing TOR signaling rescued PD phenotypes in Drosophila by decreasing S6 kinase-mediated 5'-Cap-dependent translation [45], and increasing 4E-BP-promoted 5'-Cap-independent translation [46]. Similarly, we speculate that Pi3K21B heterozygosity promotes 5'-Cap-independent translation by reducing TOR signaling, thus increasing the production of pro-survival factors leading to the suppression of PD phenotypes.

Characterization of the suppressors of the Pink1-RNAi- induced wing phenotype also identified β4GalNAcTA as a novel PD-interacting gene. β4GalNAcTA encodes for a β 1,4-N acetlygalactosaminyltransferase that mediates the N-glycosylation of protein substrates [47]. Drosophila adult mutants of β4GalNAcTA display severe locomotion abnormalities such as a low climbing index and coordination defects [48]. Glycosylation may affect protein function by diverse mechanisms, such as promoting protein stability, enabling protein recognition, altering ligand affinity and inhibiting protein activity [49]. For instance, abnormal glycosylation of alpha-dystroglycan interferes with its function leading to congenital muscular dystrophy [50]. Glycosylation may also contribute to the misfolding and accumulation of several proteins implicated in neurodegenerative disorders. For instance, glycosylation of tau and amyloid precursor protein (APP) may promote the formation and accumulation of pathogenic advanced glycosylation end-products (AGEs) [51]. In addition, α-synuclein, the primary component of Lewy bodies in Parkinson's disease, is also modified by glycosylation [9]. This modification is hypothesized to affect the clearance of α-synuclein aggregates [9]. We speculate that glycosylation mediated by β4GalNAcTA affects the stability and/or activity of components in the PD pathways, which may contribute to the accumulation of toxic proteins, increased sensitivity to oxidative damage and mitochondrial dysfunction. Future studies will be needed to elucidate the exact action of β4GalNAcTA in the PD pathways.

Conclusion

Systematic genetic screens covering ~80% of the entire genome were performed to identify modifiers of the PD phenotype in Drosophila. From the screen, we identified a number of cytological regions that interact with park and/or Pink1. Fine mapping in selected PD-interacting cytological regions was performed, which identified debra, Pi3K21B and β4GalNAcTA as novel PD-interacting genes. Future characterization of other PD-interacting cytological regions will likely lead to the identification of additional PD-interacting genes.

Declarations

Acknowledgements

We thank people in the labs of Yong Rao and Don van Meyel for suggestions and comments; the Bloomington Stock Center, VDRC, D. van Meyel, N. Haines, T. Fon and M. Guo for fly stocks. This work was supported by a Team grant from Neuroscience Canada, and an operating grant (MOP-14688) awarded to Yong Rao from Canadian Institutes of Health Research.

Authors’ Affiliations

(1)
Department of Biology, McGill University Health Centre
(2)
McGill Centre for Research in Neuroscience, Department of Neurology and Neurosurgery, Department of Medicine, McGill University Health Centre

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