Candida albicans PPR proteins are required for the expression of respiratory Complex I subunits

May combine two claims.

In Cappr13Δ, NAD4L and NAD5 probe signals are lost; other mRNAs and rRNAs were not affected; native level restored by reintroducing WT CaPPR13.

“In the Cappr13Δ mutant, we observed the loss of signal detected by the NAD4L and NAD5 probes (Fig. 4a) that hybridize to a single bicistronic transcript (Kolondra et al. 2015). Other mRNAs and rRNAs were not affected by the deletion of CaPPR13 (Supplementary Fig. 6). We could restore the native level of the NAD4L–NAD5 bicistron by reintroducing the WT CaPPR13 allele.”

• cites Kolondra et al. 2015 sourceNot checked yet

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May combine two claims.

On glycerol, all pprΔ mutants hardly grew in the presence of SHAM; on glucose, SHAM did not affect Cappr4Δ, Caaep3Δ, Cappr13Δ and slowed Cappr7Δ and Cappr11Δ.

“On glucose, SHAM did not affect the growth of Cappr4Δ, Caaep3Δ, and Cappr13Δ and slowed down the growth of Cappr7Δ and Cappr11Δ. Strikingly, on glycerol, all pprΔ mutants hardly grew in the presence of SHAM (Fig. 2a).”

May combine two claims.

No detectable CI activity in Cappr4Δ, Cappr11Δ, and Cappr13Δ; significantly decreased in Cappr7Δ; Caaep3Δ has WT level of CI activity.

“Our results show no detectable CI activity in the Cappr4Δ, Cappr11Δ, and Cappr13Δ strains, and a significantly decreased activity in Cappr7Δ, in contrast to Caaep3Δ which has a WT level of CI activity (Fig. 6a).”

May combine two claims.

Translation of all mitochondrially encoded proteins in the CaPPR7 knockout strain is dramatically decreased, and absence of CaAep3p causes a similar but less severe general translation defect.

“Translation of all mitochondrially encoded proteins in the CaPPR7 knockout strain is dramatically decreased, and the absence of CaAep3p causes a similar, albeit less severe general translation defect.”

May combine two claims.

In Caaep3Δ, ATP6-ATP8 mRNA is dramatically decreased; rRNAs, mature COX1, and ATP9 mRNAs were not affected; all other protein-coding transcript levels were decreased.

“Indeed, in the Caaep3Δ strain, we observed a dramatic decrease in the ATP6–ATP8 mRNA (Fig. 5a). Both ribosomal RNAs (Fig. 5b), as well as the mature COX1 and, interestingly, ATP9 mRNAs were not affected, whereas all the other protein-coding transcript levels were decreased (Fig. 5c).”

May combine two claims.

CI quantity is not detectable in Cappr4Δ, Cappr11Δ, and Cappr13Δ, and decreased in Cappr7Δ.

“We also evaluated the quantity of CI by Coomassie staining of native gels, showing that CI is not detectable in Cappr4Δ, Cappr11Δ, and Cappr13Δ, and decreased in Cappr7Δ (Fig. 6d).”

May combine two claims.

Cappr7Δ and Cappr11Δ showed no visible growth on glycerol at 3 days, while Cappr4Δ, Cappr13Δ, and Caaep3Δ had a less pronounced growth defect.

“Standard incubation time of 3 days revealed no visible growth on the glycerol medium for Cappr7Δ and Cappr11Δ, while a less pronounced growth defect was observed for Cappr4Δ, Cappr13Δ, and Caaep3Δ.”

May combine two claims.

Cytochrome spectra of Cappr4Δ, Cappr11Δ, and Cappr13Δ showed a WT pattern except an increased peak for cytochrome aa3; Cappr7Δ lacked cytochrome c1 and b peaks with slightly decreased aa3; Caaep3Δ had lower levels of aa3.

“For Cappr4Δ, Cappr11Δ, and Cappr13Δ, we observed a WT pattern of cytochrome spectra, except an increased peak for cytochrome aa3. Cappr7Δ spectra lacked cytochrome c1 and b peaks, while the level of aa3 decreased slightly, while Caaep3Δ revealed lower levels of cytochrome aa3.”

May combine two claims.

Deletion of CaPPR7 causes decrease of mature COB mRNA and accumulation of splicing intermediates containing intron I; other intron-containing transcripts (COX1, RNL) were not affected; ATP6, ATP8, ATP9 and other transcripts unchanged.

“Deletion of CaPPR7 led to a striking decrease of the mature COB mRNA with concomitant accumulation of the splicing intermediates (Fig. 4b). Hybridization with the intronic probe indicated that the accumulating precursor contained the first intron (COBI1; Fig. 4c). In contrast, the other transcripts containing introns (COX1 and RNL) were not affected in the CaPPR7 deletion strain (Supplementary Fig”

May combine two claims.

Cappr7Δ displays a pleiotropic phenotype: strongly reduced CI amount and activity, no detectable CIII activity, strongly reduced CIV activity, and decreased CV level with Fo/F1 dissociation.

“The Cappr7Δ strain, on the other hand, displays a pleiotropic phenotype, with a strongly reduced amount and activity of CI, no detectable CIII activity, strongly reduced CIV activity, and a decreased CV level (concomitant with dissociation of the Fo and F1 sectors).”

May combine two claims.

Caaep3Δ exhibits a strong defect of ATP synthase biogenesis, evidenced by weaker CV band, reduced ATPase activity, and dissociation into Fo and F1 subunits.

“The Caaep3Δ strain exhibits a strong defect of ATP synthase biogenesis, as evidenced by the weaker CV band on the native gel and a reduced ATPase activity, with concomitant dissociation of the complex into the Fo and F1 subunits (Fig. 6c).”

May combine two claims.

Some GFP fusion protein signal was visible in the cytoplasm, particularly for CaPpr7-GFP and CaPpr13-GFP, but close to background for CaPpr4-GFP, CaPpr11-GFP, and CaAep3-GFP.

“Some GFP fusion protein signal was also visible in the cytoplasm. The cytoplasmic signal was particularly apparent in the case of CaPpr7-GFP and CaPpr13-GFP, but close to the background level for CaPpr4-GFP, CaPpr11-GFP, and CaAep3-GFP.”

May combine two claims.

The Caaep3Δ strain showed decreased peaks of cytochrome spectra, an ATPase assembly defect, and reduced translation.

“In our experiments, the Caaep3Δ strain showed decreased peaks of cytochrome spectra, an ATPase assembly defect, and reduced translation, suggesting a more general role in protein synthesis.”

May combine two claims.

The Caaep3Δ phenotype is fully reversible in C. albicans, unlike in S. cerevisiae.

“but unlike in S. cerevisiae, it is fully reversible”

May combine two claims.

Cappr7Δ and Caaep3Δ show a similar phenotype, distinct from Cappr4Δ, Cappr11Δ and Cappr13Δ, displaying better growth when relying on CaAoxp activity, and no growth on glycerol upon its inhibition by SHAM.

“Cappr7Δ and Caaep3Δ show a similar phenotype, distinct from Cappr4Δ, Cappr11Δ and Cappr13Δ, displaying better growth when relying on CaAoxp activity, and no growth on glycerol upon its inhibition by SHAM.”

May combine two claims.

AOX2 likely rescues respiratory defects and compensates for oxidative stress.

“We also show that C. albicans cells lacking PPR proteins express a higher level of the inducible alternative oxidase (AOX2) which likely rescues respiratory defects and compensates for oxidative stress.”

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

Mutations that affect mitochondrial functions can potentially cause avirulence or have an impact on susceptibility to antifungal drugs.

“Mutations that affect mitochondrial functions can potentially cause avirulence or have an impact on susceptibility to antifungal drugs (Sun et al. 2019).”

• cites Sun et al. 2019 sourceNot checked yet

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Probably not a substantial claim: may not pass S3 (load-bearing).

The AOX is believed to confer protection against oxidative damage.

“The AOX is therefore believed to confer protection against oxidative damage (Helmerhorst et al. 2002).”

• cites Helmerhorst et al. 2002 sourceNot checked yet

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Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

In C. albicans, AOX is encoded by 2 nuclear genes, the constitutively expressed CaAOX1 and the inducible CaAOX2, induced by CRC inhibitors and reactive oxygen species.

“In C. albicans, AOX is encoded by 2 nuclear genes, the constitutively expressed CaAOX1 and the inducible CaAOX2, induced by CRC inhibitors and reactive oxygen species.”

• cites Helmerhorst et al. 2002 sourceNot checked yet

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Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

In addition to the classical respiratory chain (CRC), C. albicans possesses an alternative oxidase (AOX) and a parallel respiratory chain (PAR).

“In addition to the classical respiratory chain (CRC), C. albicans possesses an alternative oxidase (AOX) and a parallel respiratory chain (PAR) (Milani et al. 2001; Helmerhorst et al. 2002; Ruy et al. 2006).”

• cites Milani et al. 2001 sourceNot checked yet

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• cites Helmerhorst et al. 2002 sourceNot checked yet

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• cites Ruy et al. 2006 sourceNot checked yet

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The quote only partly states this claim.

Reconstitution of target ORFs into knockout strains confirmed that the observed phenotype was an effect of the deletion of the gene of interest.

“To confirm that the observed phenotype was an effect of the deletion of the gene of interest, we reintroduced target ORFs back into the genome of the knockout strain.”

May combine two claims.

Cytochrome spectra suggest a respiratory chain defect involving CIII and CIV formation in Cappr7Δ and CIV in Caaep3Δ.

“Cytochrome spectra of Cappr7Δ and Caaep3Δ show a similar phenotype for cytochrome aa3 (Fig. 2b), suggesting a defect of the respiratory chain, particularly involving the formation of CIII and CIV (in Cappr7Δ) and CIV (in Caaep3Δ).”

May combine two claims.

Lack of ATP6 and ATP8 subunits explains the respiratory-deficient phenotype of Caaep3Δ, probably due to a defect in ATP synthase biogenesis; the nonspecific decrease of multiple mitochondrial mRNAs is likely secondary to the ATP synthase defect.

“The lack of 2 important subunits of the ATP synthase explains the respiratory-deficient phenotype of Caaep3Δ strain, probably caused by the defect of the ATP synthase biogenesis. The nonspecific decrease of multiple mitochondrial mRNA levels is likely secondary to the defect of ATP synthase.”

May combine two claims.

Strains expressing only GFP fusion variants of PPR proteins had growth similar to WT, suggesting the tagged alleles were functional and did not affect native cellular localization.

“The growth phenotype of strains expressing only the GFP fusion variants was similar to that of the wild type (WT), suggesting that the modified alleles under their native promoters were functional, supporting respiratory functions and not affecting the native cellular localization of the analyzed PPR proteins (Supplementary Fig. 1a and b).”

Probably not a substantial claim: may not pass S3 (load-bearing).

Identification of particular proteins in the in organello translation assay is only tentative because mitochondrial translation had not been studied as extensively in C. albicans and no specific antibodies are available.

“As mitochondrial translation had not been studied in C. albicans as extensively as in other model systems, and no specific antibodies recognizing respiratory complex subunits in this species are available, identification of particular proteins in this assay is only tentative.”

Classified as probably not a substantial claim. May combine two claims.

CaAep3p is an ortholog of ScAep3p, which stabilizes the ATP6-ATP8 bicistronic transcript and facilitates translation of ATP8 in S. cerevisiae.

“CaAep3p is an ortholog of ScAep3p, known to stabilize the ATP6–ATP8 bicistronic transcript and specifically facilitate translation of ATP8 in S. cerevisiae.”

Probably not a substantial claim: may not pass S3 (load-bearing).

Biochemical analysis of PPR proteins is very challenging due to low expression levels and aggregation.

“Biochemical analysis of PPR proteins is very challenging due to low expression levels and aggregation (Krause et al. 2004; Coquille et al. 2014).”

• cites Krause et al. 2004 sourceNot checked yet

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• cites Coquille et al. 2014 sourceNot checked yet

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May combine two claims.

C. albicans PPR proteins of interest have largely α-helical structures containing 9 to 16 PPR motifs, typical of the PPR family.

“This indicates that our proteins of interest have properties typical for the PPR family, with a largely α-helical structure containing 9 to 16 PPR motifs.”

Probably not a substantial claim: may not pass S3 (load-bearing).

Purification of individual members of the PPR family (heterologously expressed) was possible mostly for abundant or ribosome-associated proteins, e.g. ScDmr1p or ScRmd9p.

“Purification of individual members of the PPR family (heterologously expressed) was possible mostly for abundant or ribosome-associated proteins, e.g. ScDmr1p (Puchta et al. 2010; Piątkowski and Golik 2020) or ScRmd9p (Hillen et al. 2021).”

• cites Puchta et al. 2010 sourceNot checked yet

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• cites Piątkowski and Golik 2020Not checked yet

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• cites Hillen et al. 2021 sourceNot checked yet

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May combine two claims.

Cappr4Δ and Cappr11Δ have no important changes in mitochondrially encoded transcripts, so their respiratory phenotypes might result from a general or specific translation defect.

“We did not detect any important changes in mitochondrially encoded transcripts in Cappr4Δ and Cappr11Δ (Supplementary Figs. 4 and 5), leading us to believe that the respiratory phenotypes of these strains might rather be the result of a general or specific translation defect.”

Probably not a substantial claim: may not pass S3 (load-bearing).

Mitochondrial translation experiments included a negative control with chloramphenicol to inhibit mitochondrial translation.

“For the negative control, samples were prepared similarly but in the presence of 100 µg/mL of chloramphenicol (for inhibition of mitochondrial translation).”

Classified as probably not a substantial claim.

The reconstituted strains were verified by PCR confirming the presence of the functional gene at the target locus.

“The reconstituted strains were verified by PCR which confirmed the presence of the functional gene at the target locus.”

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

Thirteen putative C. albicans PPR proteins were identified using the SCIPHER algorithm by Lipinski et al. (2011), and 9 of them show clear orthology to well-characterized PPR proteins of S. cerevisiae and S. pombe.

“Thirteen putative C. albicans PPR proteins were identified using the SCIPHER algorithm by Lipinski et al. (2011), and 9 of them show clear orthology to well-characterized PPR proteins of S. cerevisiae and S. pombe (CaAep3p, CaAep2p, CaDmr1p, CaRpo41p, CaPet111p, CaPet309p, CaAtp22p, CaRmd9p, and CaCbp1p) (Kühl et al. 2011; Lipinski et al. 2011; Herbert et al. 2013).”

• cites Lipinski et al. 2011 sourceNot checked yet

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• cites Kühl et al. 2011Not checked yet

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• cites Herbert et al. 2013 sourceNot checked yet

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Probably not a substantial claim: may not pass S3 (load-bearing).

The genotypes of obtained knockouts were confirmed by PCR.

“The genotypes of obtained knockouts were confirmed by PCR.”

May combine two claims.

Assays of CIII, CIV, and CV in Cappr4Δ, Cappr11Δ, and Cappr13Δ show no major changes compared to WT, indicating that CaPpr4p, CaPpr11p, and CaPpr13p are specifically involved in the expression of mitochondrially encoded CI subunits.

“Assays of CIII, CIV, and CV in the Cappr4Δ, Cappr11Δ, and Cappr13Δ strains show no major changes compared to WT (Fig. 6b and c; Supplementary Fig. 8), indicating that CaPpr4p, CaPpr11p, and CaPpr13p are specifically involved in the expression of mitochondrially encoded CI subunits.”

Probably not a substantial claim: may not pass S3 (load-bearing).

Results presented here are the first systematic analysis of PPR proteins in C. albicans.

“Results presented here are the first systematic analysis of PPR proteins in C. albicans, representing a budding yeast lineage that diverged prior to the loss of mitochondrially encoded CI in the Saccharomycetaceae clade and the subsequent whole-genome duplication that occurred in the ancestor of Saccharomyces.”

Classified as probably not a substantial claim.

Assignment of SDS-PAGE bands to particular mitochondrially encoded subunits was performed only tentatively based on migration of orthologous proteins.

“Assignment of obtained SDS–PAGE bands to particular mitochondrially encoded subunits was therefore performed only tentatively based on migration of orthologous proteins from other model systems, in particular S. cerevisiae and animals (Barrientos et al. 2002; Chiron et al. 2005; Kühl et al. 2011; Baggio et al. 2014).”

Classified as probably not a substantial claim. May combine two claims.

PPR proteins are composed of tandem antiparallel repeated α-helices, which form a superhelix enclosing the central groove for RNA substrate binding; this structural fold is a defining feature of PPR family members rather than a conserved sequence.

“PPR proteins are composed of tandem antiparallel repeated α-helices, which form a superhelix enclosing the central groove for RNA substrate binding. This structural fold is a defining feature of PPR family members, rather than a conserved sequence (Small and Peeters 2000).”

• cites Small and Peeters 2000Not checked yet

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May combine two claims.

C. albicans is an obligate diploid which does not propagate extrachromosomal elements such as plasmids.

“C. albicans is an obligate diploid which does not propagate extrachromosomal elements such as plasmids (Noble and Johnson 2007; Samaranayake and Hanes 2011).”

• cites Noble and Johnson 2007Not checked yet

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• cites Samaranayake and Hanes 2011Not checked yet

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Classified as probably not a substantial claim.

Cappr11ΔMTS was introduced to control whether the reconstitution phenotype was not caused by restoring the functional CaUra3p enzyme.

“Cappr11ΔMTS gene without the mitochondrial localization signal (MTS) sequence was introduced to control whether the reconstitution phenotype was not caused by restoring the functional CaUra3p enzyme.”

Probably not a substantial claim: may not pass S3 (load-bearing).

It is hard to conclude whether the translation defect in Cappr7Δ and Caaep3Δ is primary or just an indirect result of altered transcription and ATP reduction.

“In the case of both proteins, it is hard to conclude whether the translation defect is primary or just an indirect result of altered transcription and ATP reduction, caused by inefficient respiratory chain activity.”

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

Three repetitions of each measurement were performed and analyzed statistically.

“Three repetitions of each measurement were performed and analyzed statistically.”

May combine two claims.

CaPpr4p, CaPpr7p, CaPpr11p, CaPpr13p, and CaAep3p localize to mitochondria.

“The GFP signals revealed a typical elongated mitochondrial network which colocalized with MitoTracker, but not with Hoechst-stained nuclei (Fig. 1b), confirming the mitochondrial localization of these PPR proteins.”

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

Knowledge of protein structure is necessary to identify new PPR proteins and fully predict the number of PPR repeats in already identified family members.

“Therefore, knowledge of protein structure is necessary to identify new PPR proteins and fully predict the number of PPR repeats in already identified family members.”

Probably not a substantial claim: may not pass S3 (load-bearing).

Partitioning electron flux between the 3 respiratory pathways probably allows C. albicans cells to control energetic and redox status.

“Partitioning electron flux between the 3 respiratory pathways probably allows C. albicans cells to control energetic and redox status (Milani et al. 2001; Helmerhorst et al. 2005; Ruy et al. 2006).”

• cites Milani et al. 2001 sourceNot checked yet

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• cites Helmerhorst et al. 2005 sourceNot checked yet

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• cites Ruy et al. 2006 sourceNot checked yet

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Classified as probably not a substantial claim.

PPR proteins play an important role in the control of eukaryotic mitochondrial gene expression, including transcript end maturation, splicing, editing, RNA stabilization, and transcriptional and translational activation.

“Pentatricopeptide repeat (PPR) proteins play an important role in the control of eukaryotic mitochondrial gene expression, including transcript end maturation, splicing, editing, RNA stabilization, and transcriptional and translational activation (Schmitz-Linneweber and Small 2008; Lipinski et al. 2011; Kühl et al. 2011; Herbert et al. 2013; Wang et al. 2017; Barros and Tzagoloff 2017; Seshadri et”

• cites Schmitz-Linneweber and Small 2008Not checked yet

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• cites Lipinski et al. 2011 sourceNot checked yet

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• cites Kühl et al. 2011Not checked yet

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May combine two claims.

NAD4L-NAD5 mRNA is the specific target of CaPpr13, which is required for its stability.

“We therefore postulate that the NAD4L–NAD5 mRNA is the specific target of the CaPpr13 protein which is required for its stability (Fig. 4a).”

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

RNA transfer accuracy and loading control were assessed by methylene blue staining.

“For transfer accuracy and loading control, RNA was stained with methylene blue (0.02% methylene blue, 0.3 M sodium acetate pH 5.2).”

May combine two claims.

The absence of the 4 mitochondrially localized PPR proteins leads to a respiratory deficiency and impairs CI formation.

“The absence of these proteins leads to a respiratory deficiency and impairs CI formation.”

May combine two claims.

In C. albicans, ATP9, ATP6, and ATP8 originate from a single polycistronic transcription unit (TU4) controlled by the same promoter and later separated into ATP9 and the bicistronic ATP6-ATP8 mRNA, whereas in S. cerevisiae they are transcribed separately.

“In C. albicans, ATP9, ATP6, and ATP8 originate from a single polycistronic transcription unit (TU4) controlled by the same promoter and later separated into ATP9 and the bicistronic ATP6–ATP8 mRNA, whereas in S. cerevisiae, ATP9 and the ATP6–ATP8 bicistron are transcribed separately (Kolondra et al. 2015; Golik 2024).”

• cites Kolondra et al. 2015 sourceNot checked yet

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• cites Golik 2024 sourceNot checked yet

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Probably not a substantial claim: may not pass S3 (load-bearing).

Respiratory growth of C. albicans strains expressing PPR-GFP fusions was tested to confirm that the fusion proteins were functional.

“Respiratory growth of C. albicans strains expressing the fusions was tested to confirm that the PPR–GFP fusion proteins were functional.”

May combine two claims.

All tested pprΔ mutants are viable, suggesting that the PPR proteins described are not required for mtDNA maintenance but participate in gene expression.

“At the same time, all tested pprΔ mutants are viable which in a petite-negative yeast suggests that the PPR proteins described herein are not required for mtDNA maintenance, but participate in gene expression.”

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims. The quote only partly states this claim.

The northern blot experiment for CaAOX2 was repeated 3 times, and a representative result is shown.

“The experiment was repeated 3 times, and a representative result is shown.”

Probably not a substantial claim: may not pass S3 (load-bearing).

Ncu20711 is a PPR protein required for ND1-ND4 splicing in N. crassa.

“An example of such regulation is provided by Ncu20711, a PPR protein required for ND1–ND4 splicing in N. crassa (Solotoff et al. 2015).”

• cites Solotoff et al. 2015 sourceNot checked yet

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May combine two claims.

In Cappr13Δ, the NAD4L-NAD5 transcript cannot be detected, suggesting it is not transcribed or rapidly degraded.

“In the mutant strain that lacks the CaPpr13 protein, this transcript cannot be detected, suggesting that it is not transcribed or rapidly degraded.”

Classified as probably not a substantial claim. May combine two claims. The quote only partly states this claim.

Quantification of CaAOX2 mRNA was performed for 3 independent experiments and analyzed statistically.

“Quantification was performed for 3 independent experiments and analyzed statistically.”

May combine two claims.

CIII deficiency affects downstream elements of the respiratory chain, CIV, and particularly the ATP synthase.

“CIII deficiency affects downstream elements of the respiratory chain, CIV, and particularly the ATP synthase.”

May combine two claims.

The altered stoichiometry and biogenesis defect of CIII is caused by the deficiency of its only mitochondrially encoded subunit COB and results in the observed loss of CIII activity.

“The altered stoichiometry and biogenesis defect of CIII is caused by the deficiency of its only mitochondrially encoded subunit COB and results in the observed loss of CIII activity.”

Probably not a substantial claim: may not pass S3 (load-bearing).

Plant P-type PPR proteins are associated with RNA splicing.

“Similarly, plant P-type PPR proteins are associated with RNA splicing, for example,OsNbl3 (Qiu et al. 2021), AtPpr19 (Lee et al. 2017), AtOtp439, and AtTang2 (Colas des Francs-Small et al. 2014).”

• cites Qiu et al. 2021 sourceNot checked yet

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• cites Lee et al. 2017 sourceNot checked yet

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• cites Colas des Francs-Small et al. 2014 sourceNot checked yet

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May combine two claims.

The stop codon of NAD4L is contiguous with the start codon of downstream NAD5, and the two mRNAs are co-translated.

“The stop codon of NAD4L is contiguous with the start codon of downstream NAD5. It is rather clear that the 2 mRNA are co-translated (Kolondra et al. 2015), as we do not detect individual NAD4L and NAD5 transcripts.”

• cites Kolondra et al. 2015 sourceNot checked yet

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Probably not a substantial claim: may not pass S3 (load-bearing).

The shift from transcriptional control to posttranscriptional regulation is evolutionarily advanced compared to prokaryotic ancestors that lack PPR proteins.

“The shift from transcriptional control to posttranscriptional regulation is considered evolutionarily advanced compared to prokaryotic ancestors which do not contain PPR proteins (Ott et al. 2016; Siira et al. 2017; Seshadri et al. 2020).”

• cites Ott et al. 2016 sourceNot checked yet

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• cites Siira et al. 2017 sourceNot checked yet

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• cites Seshadri et al. 2020 sourceNot checked yet

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Classified as probably not a substantial claim. May combine two claims.

In fungi, mitochondrially encoded NADH dehydrogenase subunits are often cotranscribed as bicistronic mRNAs; in C. albicans as NAD6-NAD1, NAD2-NAD3, and NAD4L-NAD5.

“In fungi, mitochondrially encoded NADH dehydrogenase subunits are often cotranscribed as bicistronic mRNAs, in the case of C. albicans as NAD6–NAD1, NAD2–NAD3, and NAD4L–NAD5 (Kolondra et al. 2015).”

• cites Kolondra et al. 2015 sourceNot checked yet

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Probably not a substantial claim: may not pass S3 (load-bearing).

SpPpr10p plays a general role in the initiation of mitochondrial protein synthesis.

“SpPpr10p plays a general role in the initiation of mitochondrial protein synthesis, as the deletion strain shows impaired translation of all mitochondrial mRNAs.”

Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

CaPpr7 is the first C. albicans protein involved in splicing in mitochondria.

“The CaPpr7 protein would be the first C. albicans protein involved in splicing in mitochondria.”

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

ScMrx1p is associated with ribosomes during translation and coupled to the mitochondrial membrane by the MIOREX complex.

“ScMrx1p is associated with ribosomes during translation, coupled to the mitochondrial membrane by the MIOREX complex (Kehrein et al. 2015).”

• cites Kehrein et al. 2015 sourceNot checked yet

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May combine two claims.

Knockout of NCU08674 does not exhibit specific respiratory complex impairment but causes a translational defect that decreases levels of all electron transport chain complexes.

“The knockout of NCU08674 does not exhibit specific respiratory complex impairment, but rather a translational defect that causes a decreased level of all electron transport chain complexes.”

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

Deletion of SpPPR10 causes a reduction in some mitochondrial transcripts and a partial loss of mtDNA.

“Deletion of the SpPPR10 gene causes a reduction in some mitochondrial transcripts and a partial loss of mtDNA (Wang et al. 2017).”

• cites Wang et al. 2017 sourceNot checked yet

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Probably not a substantial claim: may not pass S3 (load-bearing).

Transcription and translation in fungal mitochondria are closely connected by the RNA processing machinery.

“Transcription and translation in fungal mitochondria are believed to be closely connected by the RNA processing machinery (Singh et al. 2020), which partially explains the lower level of multiple mitochondrial transcripts in the Cappr7Δ strain.”

• cites Singh et al. 2020 sourceNot checked yet

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Probably not a substantial claim: may not pass S3 (load-bearing).

SpPpr10p mediates the association of translation initiation factors SpMti2p, SpMti3p, and SpMpa1 with the small mitoribosome subunit.

“SpPpr10p was reported to mediate the association of translation initiation factors (SpMti2p, SpMti3p, and the SpMpa1 matrix protein) with the small mitoribosome subunit (mt-SSU) (Liu et al. 2020; Luo et al. 2021).”

• cites Liu et al. 2020 sourceNot checked yet

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• cites Luo et al. 2021 sourceNot checked yet

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Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

The S. pombe CaAep3p homolog SpPpr7p is responsible for stabilization of SpATP6 mRNA, and its absence causes a reduction in mitochondrial protein synthesis.

“The CaAep3p homolog of S. pombe (SpPpr7p) is responsible for the stabilization of SpATP6 mRNA, and its absence causes a reduction in mitochondrial protein synthesis (Kühl et al. 2011), which supports our conclusions about CaAEP3 function.”

• cites Kühl et al. 2011Not checked yet

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Probably not a substantial claim: may not pass S3 (load-bearing).

The mitochondrial defect in CapprΔ strains must be signaled to the nucleus, possibly by a retrograde pathway triggered by ROS production.

“The mitochondrial defect in the CapprΔ strains must be signaled to the nucleus, possibly by a form of the retrograde pathway triggered by ROS production.”

Probably not a substantial claim: may not pass S3 (load-bearing).

Some cytosolic signal cannot be excluded as corresponding to fusion proteins translated and folded in the cytoplasm prior to mitochondrial import.

“although we cannot exclude that some of the cytosolic signal corresponds to the fusion proteins translated and folded in the cytoplasm prior to the mitochondrial import.”

Probably not a substantial claim: may not pass S3 (load-bearing).

CaAoxp is an enzyme protecting against ROS.

“CaAoxp is thought to be an enzyme protecting against ROS (Yan et al. 2009; Rogov et al. 2014), which might be relevant, as dysfunctional Cl and CIII generate more free oxygen radicals (Li et al. 2011).”

• cites Yan et al. 2009 sourceNot checked yet

  Not checked in the free run.

• cites Rogov et al. 2014 sourceNot checked yet

  Not checked in the free run.

May combine two claims.

CaAoxp acts downstream of CI and does not generate a proton gradient, so it cannot entirely bypass the loss of CI.

“CaAoxp acts downstream of CI and does not generate a proton gradient, so it cannot entirely bypass the loss of CI.”

Probably not a substantial claim: may not pass S3 (load-bearing).

General regulators of mitochondrial transcription and translation should be more abundant than specific regulators present in fewer copies.

“General regulators of mitochondrial transcription and translation should be more abundant, in contrast to specific regulators present in fewer copies (Kühl et al. 2011).”

• cites Kühl et al. 2011Not checked yet

  Not checked in the free run.

May combine two claims.

CaAEP3 is an evolutionarily conserved gene that shares the function of its S. cerevisiae and S. pombe homologs but does not play a specific role in CI biogenesis.

“A striking observation concerning CaAEP3 is that as an evolutionary conserved gene, it shares the function of its S. cerevisiae and S. pombe homologs, but does not play a specific role in CI biogenesis.”

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

Fungal PPR proteins localize to mitochondria, and some remain in close association with mitochondrial membranes.

“Fungal PPR proteins localize to mitochondria, and some of them remain in close association with the mitochondrial membranes (Kühl et al. 2011; Barros and Tzagoloff 2017; Jumper et al. 2021).”

• cites Kühl et al. 2011Not checked yet

  Not checked in the free run.

• cites Barros and Tzagoloff 2017Not checked yet

  Not checked in the free run.

• cites Jumper et al. 2021 sourceNot checked yet

  Not checked in the free run.

May combine two claims.

PPR proteins participate in mitochondrial gene expression as accessory factors but are not structural components of highly abundant complexes like the mitoribosome.

“suggesting that they participate in the mitochondrial gene expression as accessory factors, but are not structural components of highly abundant complexes like the mitoribosome.”

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

Dramatic induction of AOX under respiratory-stress conditions broadens metabolic flexibility of C. albicans and enables pathogenesis.

“Dramatic induction of AOX under respiratory-stress conditions, impairing the classical electron transport chain, was recently shown to broaden the metabolic flexibility of C. albicans and enable pathogenesis (Liu et al. 2023).”

• cites Liu et al. 2023 sourceNot checked yet

  Not checked in the free run.

Probably not a substantial claim: may not pass S3 (load-bearing).

The low expression of fusion constructs necessitated long exposure for visualization, which likely enhanced background fluorescence in the cytoplasm.

“The low expression of fusion constructs necessitated long exposure for visualization, which likely also enhanced the background fluorescence observed in the cytoplasm, although we cannot exclude that some of the cytosolic signal corresponds to the fusion proteins translated and folded in the cytoplasm prior to the mitochondrial import.”

May combine two claims.

CaAoxp appears crucial for C. albicans survival under nonfermentable conditions despite loss of CI activity, suggesting it participates in the rescue mechanism.

“The CaAoxp appears to be crucial in this situation, suggesting that the enzyme participates in the rescue mechanism.”

Probably not a substantial claim: may not pass S3 (load-bearing).

It is difficult to determine whether C. albicans PPR proteins are associated with the membrane fraction due to lack of available antibodies.

“However, it is difficult to determine whether they are associated with the membrane fraction, due to the lack of available antibodies that detect C. albicans mitochondrial proteins which would be required for sub-mitochondrial fractionation experiments.”

May combine two claims.

The expectation that general regulators are more abundant is not the rule, as CaPpr7p shows very low expression but exhibits a general translation defect in the mutant strain.

“That seems, however, not to be the rule, as seen by the example of CaPpr7p showing a very low expression level, but exhibiting a general translation defect in the mutant strain.”

May combine two claims.

All PPR-GFP fusion proteins investigated were expressed under their native promoters, so the intensity of observed fluorescence should reflect their expression levels.

“All the PPR–GFP fusion proteins investigated by us were expressed under their native promoters, so the intensity of the observed fluorescence signal should reflect their expression levels.”

May combine two claims.

Potential alternative dehydrogenases and the PAR pathway could compensate for CRC dysfunction in C. albicans.

“On the other hand, potential alternative dehydrogenases (Antos-Krzeminska and Jarmuszkiewicz 2019) and the PAR pathway (Helmerhorst et al. 2002; Ruy et al. 2006) could compensate for the CRC dysfunction in C. albicans.”

• cites Antos-Krzeminska and Jarmuszkiewicz 2019Not checked yet

  Not checked in the free run.

• cites Helmerhorst et al. 2002 sourceNot checked yet

  Not checked in the free run.

• cites Ruy et al. 2006 sourceNot checked yet

  Not checked in the free run.

Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

The retention of mitochondrial-encoded subunits of respiratory chain complexes is correlated with the repertoire of PPR proteins.

“It is in line with our expectations that the retention of mitochondrial-encoded subunits of respiratory chain complexes is correlated with the repertoire of PPR proteins.”

May combine two claims.

PPR proteins such as CaPpr4, CaPpr11, and CaPpr13 important for CI expression are gained or lost in evolution of different lineages, as they perform functions required only when relevant mitochondrial genome features are present.

“The PPR proteins such as CaPpr4, CaPpr11, and CaPpr13 important for the expression of CI are gained or lost in evolution of different lineages, as they perform functions that are required only when the relevant mitochondrial genome features are present.”

May combine two claims.

The presence of mitochondrially encoded CI subunits in C. albicans correlates with the evolution of nuclear-encoded PPR proteins that are required for their expression and are not found in species lacking CI, such as S. cerevisiae.

“The presence of mitochondrially encoded CI subunits in C. albicans was shown to correlate with the evolution of nuclear-encoded PPR proteins that are required for their expression and are not found in species lacking CI, such as S. cerevisiae.”

May combine two claims.

The CRC, AOX, and PAR pathways are not additive and compete for electrons, so inhibiting one would increase electron flow to the others.

“The CRC, AOX, and PAR pathways are not additive, and they compete for electrons, so inhibiting one would increase electron flow to the others.”

Probably not a substantial claim: may not pass S1 (asserted), S2 (checkable), S3 (load-bearing), S4 (based).

Compensation for respiratory deficiency by alternative pathways, mostly absent from S. cerevisiae, can be studied in the C. albicans model.

“An additional aspect of interest that can be studied in the C. albicans model is the compensation for respiratory deficiency by alternative pathways, mostly absent from S. cerevisiae.”

Probably not a substantial claim: may not pass S2 (checkable).

Harnessing C. albicans as a research model allowed searching for new factors required for mitochondrial genome expression.

“Harnessing C. albicans as a research model allowed to search for new factors required for mitochondrial genome expression.”

Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

PPR proteins conserved in evolution, like CaAep3p possessing an ortholog in S. cerevisiae, maintain their function.

“PPR proteins conserved in evolution, like CaAep3p possessing an ortholog in S. cerevisiae, maintain their function.”

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

Higher aa3 cytochrome levels could suggest induction of the PAR pathway and activation of additional cytochrome pools.

“which could suggest induction of the PAR pathway and activation of additional cytochrome pools, previously reported in Candida parapsilosis and C. albicans (Guerin et al. 1989; Ruy et al. 2006).”

• cites Guerin et al. 1989 sourceNot checked yet

  Not checked in the free run.

• cites Ruy et al. 2006 sourceNot checked yet

  Not checked in the free run.