quiescent nuclear microtubule bundle

cellstructuremech:quiescent_nuclear_microtubule_bundle · Cytoskeleton · Other · Proposed

A stable monopolar bundle of parallel nuclear microtubules formed during glucose-exhaustion-induced quiescence, characterized in Saccharomyces cerevisiae. The bundle extends from the nuclear face of the spindle pole body and reorganizes kinetochore and centromere distribution; it is distinct from the antiparallel cytoplasmic quiescent-cell bundle of fission yeast. [DOI:10.1083/jcb.201306075]

Multipanel figure: A shows tubulin and Dad2 with expansion microscopy and SIM (1 micrometer bars); K follows quiescent bundles after laser severing (2 micrometer bar). L is a proliferating-cell anaphase-spindle control, not a quiescent bundle. Other panels combine perturbation imaging, morphometry, immunoblots and survival assays. Nonspecific cytoplasmic yellow background in A is not GFP localization. OTHER · *Saccharomyces cerevisiae* (`NCBITaxon:4932`) · Damien Laporte, Aurelie Massoni-Laporte, Charles Lefranc, Jim Dompierre, David Mauboules, Emmanuel T Nsamba, Anne Royou, Lihi Gal, Maya Schuldiner, Mohan L Gupta, et al.; CC BY, via PubMed Central · CC_BY_4_0 · source: PMC PMC10963028.1 fig3s1 · `DOI:10.7554/eLife.89958`

Synonyms: Q-nMT bundle; quiescent-cell nuclear microtubule bundle

Part of: nucleus (GO:0005634); GO:0015630 — microtubule cytoskeleton (no local record)

Has part: nuclear microtubule (GO:0005880)

UniProt location names: UniProt Consortium, CC BY 4.0. Reference label and route sources.

Components

Component	Type	Part of / acts on	Grounding	Genes	Essential	Role
Alpha tubulin	Protein	part of	`InterPro:IPR002452`	TUB1, TUB3	UNKNOWN	Alpha-tubulin subunits of the nuclear bundle; Tub1 and Tub3 colocalize, with distinct contributions to assembly. `DOI:10.7554/eLife.89958` Figure 2 and its supplements localize both isotypes. Tub3 loss impairs phase-II stability, but replacing it with Tub1 restores stable, thinner bundles; Tub3 is not an obligatory unique subunit. `InterPro:IPR002452` Complete native InterPro matches checked on 2026-10-05; integrated type=family and exact class scope verified.
Beta tubulin	Protein	part of	`InterPro:IPR002453`		UNKNOWN	Beta partner class of the alpha/beta microtubule polymer; no beta-isotype localization assay is inferred. `DOI:10.1083/jcb.201306075` TEM and tubulin microscopy establish a microtubule array. `GO:0005874` The native microtubule definition specifies alpha/beta subunits; this is a polymer-class assertion, not a TUB2-specific imaging claim. `InterPro:IPR002453` Complete native InterPro matches checked on 2026-10-05; integrated type=family and exact class scope verified.
XMAP215	Protein	part of	`InterPro:IPR045110`	STU2	UNKNOWN	Microtubule-associated regulator localized at both bundle ends and occasional intermediate puncta. `DOI:10.1083/jcb.201306075` Figure 1 and Results localize Stu2 at both array ends and occasionally within the array; no bundle-specific necessity is asserted. `InterPro:IPR045110` Complete native InterPro matches checked on 2026-10-05; integrated type=family and exact class scope verified.
Bik1-like CLIP-170 microtubule-associated protein	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	BIK1	UNKNOWN	Resident microtubule-associated protein detected at both ends of the quiescent array. `DOI:10.1083/jcb.201306075` Figure 1 and Results place Bik1 at both ends and occasionally at internal dots.
Microtubule-associated protein RP/EB	Protein	part of	`InterPro:IPR027328`	BIM1	DISPENSABLE	Bundle-associated EB protein; single BIM1 deletion permits stable bundles, with conditional defects when other factors are removed. `DOI:10.1083/jcb.201306075` Bim1 localizes along the full array. `DOI:10.7554/eLife.89958` Figure 3 contrasts normal stable bundles in bim1 deletion with severe defects in bir1 bim1 and slk19 bim1 combinations. `InterPro:IPR027328` Complete native InterPro matches checked on 2026-10-05; integrated type=family and exact class scope verified.
Kar3-like kinesin-14 motor	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	KAR3	UNKNOWN	Resident motor contributing to early normal bundle assembly; motor-driven crosslinking is not directly resolved. `DOI:10.7554/eLife.89958` Figure 4 detects Kar3-3GFP at the SPB and bundle puncta; kar3 deletion leaves very short structures. This later positive assay supersedes the 2013 nondetection.
Kinesin-like protein KIF11-like	Protein	part of	`InterPro:IPR047149`	CIN8, KIP1	UNKNOWN	Resident kinesin-5 class with distinct activities: Cin8 affects phase-II bundle thickness, whereas Kip1 supports full stabilization. `DOI:10.7554/eLife.89958` Figure 4 and supplement 1 distinguish cin8 and kip1 phenotypes. Faint Cin8-GFP signal is shown with a Tub1-only channel control; Kip1 is enriched at the bundle distal end. Single deletions do not establish a whole-family assembly requirement. `InterPro:IPR047149` Complete native InterPro matches checked on 2026-10-05; integrated type=family and exact class scope verified.
Bir1-like chromosomal passenger protein	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	BIR1	UNKNOWN	Resident chromosomal passenger protein distributed along the bundle and enriched at its distal end. `DOI:10.7554/eLife.89958` Figure 3 localizes Bir1 and shows shortened, incompletely stable bundles after BIR1 loss, with a stronger combined BIM1 defect.
Sli15-like inner centromere protein	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	SLI15	UNKNOWN	Resident INCENP-like passenger protein associated with assembly and stabilization of the bundle. `DOI:10.7554/eLife.89958` Figure 3 localizes Sli15 along the bundle and at its distal end; early sli15-3 inactivation impairs assembly. Residence of Sli15 does not prove residence of every CPC subunit.
Slk19-like microtubule-associated protein	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	SLK19	UNKNOWN	Resident bundle-end protein contributing to mature bundle dimensions and stability. `DOI:10.7554/eLife.89958` Figure 3 localizes Slk19 at both ends; slk19 deletion produces shorter, thinner, nocodazole-sensitive bundles, exacerbated by BIM1 loss.

Organism-specific protein examples

Named proteins in which each component's role was established, with the organism the evidence comes from. The component above is the taxon-agnostic family; these are the specific entries behind it.

Alpha tubulin

Accession	Protein	Gene	Organism	Entry
`UniProtKB:P09733`	Tubulin alpha-1 chain	TUB1	Saccharomyces cerevisiae S288C (`NCBITaxon:559292`)	REVIEWED
Role and evidence (2 references) Reference-sequence exemplar; the accession does not assert that the exact reference stock was imaged. `DOI:10.7554/eLife.89958` Tub1 labels Q-nMT bundles throughout the study; Figure 2 compares tagged Tub1 and Tub3. `https://www.uniprot.org/uniprotkb/P09733/entry` Reviewed entry, gene and source taxon verified live on 2026-10-05; localization is supported by the primary experiment.
`UniProtKB:P09734`	Tubulin alpha-3 chain	TUB3	Saccharomyces cerevisiae S288C (`NCBITaxon:559292`)	REVIEWED
Role and evidence (2 references) Reference-sequence exemplar; the accession does not assert that the exact reference stock was imaged. `DOI:10.7554/eLife.89958` Figure 2A shows tagged Tub3 together with Tub1 in Q-nMT bundles; Figure 2 supplement 1A localizes Tub3-3GFP alongside alpha-tubulin by expansion microscopy. `https://www.uniprot.org/uniprotkb/P09734/entry` Reviewed entry, gene and source taxon verified live on 2026-10-05; localization is supported by the primary experiment.

XMAP215

Accession	Protein	Gene	Organism	Entry
`UniProtKB:P46675`	Protein STU2	STU2	Saccharomyces cerevisiae S288C (`NCBITaxon:559292`)	REVIEWED
Role and evidence (2 references) Reference-sequence exemplar; the accession does not assert that the exact reference stock was imaged. `DOI:10.1083/jcb.201306075` Stu2-GFP marks both ends of the nuclear array. `https://www.uniprot.org/uniprotkb/P46675/entry` Reviewed entry, gene and source taxon verified live on 2026-10-05; localization is supported by the primary experiment.

Bik1-like CLIP-170 microtubule-associated protein

Accession	Protein	Gene	Organism	Entry
`UniProtKB:P11709`	Nuclear fusion protein BIK1	BIK1	Saccharomyces cerevisiae S288C (`NCBITaxon:559292`)	REVIEWED
Role and evidence (2 references) Reference-sequence exemplar; the accession does not assert that the exact reference stock was imaged. `DOI:10.1083/jcb.201306075` Bik1 localization is directly reported for the nuclear array. `https://www.uniprot.org/uniprotkb/P11709/entry` Reviewed entry, gene and source taxon verified live on 2026-10-05; localization is supported by the primary experiment.

Microtubule-associated protein RP/EB

Accession	Protein	Gene	Organism	Entry
`UniProtKB:P40013`	Protein BIM1	BIM1	Saccharomyces cerevisiae S288C (`NCBITaxon:559292`)	REVIEWED
Role and evidence (2 references) Reference-sequence exemplar; the accession does not assert that the exact reference stock was imaged. `DOI:10.7554/eLife.89958` Bim1 is detected along the Q-nMT bundle; single and combined deletions distinguish redundancy. `https://www.uniprot.org/uniprotkb/P40013/entry` Reviewed entry, gene and source taxon verified live on 2026-10-05; localization is supported by the primary experiment.

Kar3-like kinesin-14 motor

Accession	Protein	Gene	Organism	Entry
`UniProtKB:P17119`	Kinesin-like protein KAR3	KAR3	Saccharomyces cerevisiae S288C (`NCBITaxon:559292`)	REVIEWED
Role and evidence (2 references) Reference-sequence exemplar; the accession does not assert that the exact reference stock was imaged. `DOI:10.7554/eLife.89958` Kar3-3GFP is directly detected along the bundle in Figure 4. `https://www.uniprot.org/uniprotkb/P17119/entry` Reviewed entry, gene and source taxon verified live on 2026-10-05; localization is supported by the primary experiment.

Kinesin-like protein KIF11-like

Accession	Protein	Gene	Organism	Entry
`UniProtKB:P27895`	Kinesin-like protein CIN8	CIN8	Saccharomyces cerevisiae S288C (`NCBITaxon:559292`)	REVIEWED
Role and evidence (2 references) Reference-sequence exemplar; the accession does not assert that the exact reference stock was imaged. `DOI:10.7554/eLife.89958` Figure 4 supplement 1B supports weak bundle-associated Cin8 signal, not uniform high occupancy; inspected native image includes the channel control. `https://www.uniprot.org/uniprotkb/P27895/entry` Reviewed entry, gene and source taxon verified live on 2026-10-05; localization is supported by the primary experiment.
`UniProtKB:P28742`	Kinesin-like protein KIP1	KIP1	Saccharomyces cerevisiae S288C (`NCBITaxon:559292`)	REVIEWED
Role and evidence (2 references) Reference-sequence exemplar; the accession does not assert that the exact reference stock was imaged. `DOI:10.7554/eLife.89958` Figure 4 places Kip1 at the distal bundle end; kip1 deletion compromises phase-III stabilization. `https://www.uniprot.org/uniprotkb/P28742/entry` Reviewed entry, gene and source taxon verified live on 2026-10-05; localization is supported by the primary experiment.

Bir1-like chromosomal passenger protein

Accession	Protein	Gene	Organism	Entry
`UniProtKB:P47134`	Chromosomal passenger complex protein BIR1	BIR1	Saccharomyces cerevisiae S288C (`NCBITaxon:559292`)	REVIEWED
Role and evidence (2 references) Reference-sequence exemplar; the accession does not assert that the exact reference stock was imaged. `DOI:10.7554/eLife.89958` Bir1 is directly localized on Q-nMT bundles in Figure 3. `https://www.uniprot.org/uniprotkb/P47134/entry` Reviewed entry, gene and source taxon verified live on 2026-10-05; localization is supported by the primary experiment.

Sli15-like inner centromere protein

Accession	Protein	Gene	Organism	Entry
`UniProtKB:P38283`	Inner centromere protein SLI15	SLI15	Saccharomyces cerevisiae S288C (`NCBITaxon:559292`)	REVIEWED
Role and evidence (2 references) Reference-sequence exemplar; the accession does not assert that the exact reference stock was imaged. `DOI:10.7554/eLife.89958` Direct Q-nMT localization and temperature-sensitive perturbation are reported in Figure 3 and supplement 1. `https://www.uniprot.org/uniprotkb/P38283/entry` Reviewed entry, gene and source taxon verified live on 2026-10-05; localization is supported by the primary experiment.

Slk19-like microtubule-associated protein

Accession	Protein	Gene	Organism	Entry
`UniProtKB:Q08581`	Kinetochore protein SLK19	SLK19	Saccharomyces cerevisiae S288C (`NCBITaxon:559292`)	REVIEWED
Role and evidence (2 references) Reference-sequence exemplar; the accession does not assert that the exact reference stock was imaged. `DOI:10.7554/eLife.89958` Slk19 localizes at both Q-nMT ends; a protein name alone is not the basis of the localization assertion. `https://www.uniprot.org/uniprotkb/Q08581/entry` Reviewed entry, gene and source taxon verified live on 2026-10-05; localization is supported by the primary experiment.

Canonical examples

NCBITaxon:4932 Saccharomyces cerevisiae — Budding yeast studied by fluorescence, expansion microscopy, laser ablation and perturbations; the 2013 defining study additionally supplies TEM. Strain backgrounds differ among assays; no all-fungi prevalence is asserted. [DOI:10.7554/eLife.89958]

Functions

Quiescent nuclear reorganization — The nuclear array supports relocation of kinetochore-centromere clusters away from the SPB and displacement of the nucleolus.
- DOI:10.1083/jcb.201306075 Kinetochore and centromere localization, plus no-array mutants, associate array formation with nuclear reorganization; chromosomes and nucleolus are not treated as bundle constituents.
Support of quiescent survival and recovery — Bundle formation contributes to survival and subsequent colony formation in the tested glucose-exhaustion conditions.
- DOI:10.1083/jcb.201306075 Array-defective mutants lose viability and regrowth capacity; pleiotropic effects limit a uniquely bundle-specific causal claim.
- DOI:10.7554/eLife.89958 Early nocodazole prevents formation and impairs survival/regrowth, whereas late treatment of stabilized bundles does not have the same effect. This narrows but does not eliminate off-target explanations.

Mechanism graphs

Glucose exhaustion and early bundle assembly (ASSEMBLY)

Physiological and perturbation-defined mechanism in S. cerevisiae; the upstream glucose-exhaustion signal and exact crosslinking reactions are unresolved.

Subject	Predicate	Object	Evidence
Glucose exhaustion	stimulates	Q-nMT bundle assembly	`DOI:10.7554/eLife.89958` Figure 1 and Results identify sequential establishment, growth and stabilization phases; exact timing depends on culture conditions.
Functional kinetochore-microtubule attachment	supports	Q-nMT bundle assembly	`DOI:10.7554/eLife.89958` Figure 3 and supplement 1 compare early and late ndc80-1 restrictive-temperature treatments.

Regulated disassembly on quiescence exit (DISASSEMBLY)

Exit from glucose-exhaustion-induced quiescence; timing and deletion evidence do not identify a molecular checkpoint. Kip3 and She1 are external regulators, not inferred stable residents.

Subject	Predicate	Object	Evidence
Glucose refeeding	stimulates	Q-nMT bundle disassembly	`DOI:10.1083/jcb.201306075` Quiescence-exit experiments compare glucose alone and cycloheximide treatment.
Kinesin-like protein KIP3	supports	Q-nMT bundle disassembly	`DOI:10.7554/eLife.89958` Figure 5 distinguishes delayed onset from post-onset depolymerization kinetics; Kip3 is resynthesized on exit.
Mitotic spindle-associated protein SHE1	supports	Q-nMT bundle disassembly	`DOI:10.7554/eLife.89958` Figure 5 compares kip3 and kip3 she1 deletions. The native spindle-associated She1 accession is P38200, not MYO4's historical SHE1 alias P32492.
Q-nMT bundle disassembly	supports	Spindle pole body separation	`DOI:10.7554/eLife.89958` Figure 5 tracks bundle disappearance and SPB separation in wild type and mutants. The combined deletion also delays separation without delaying overall proliferation; this is not proof of a specific molecular checkpoint.

Discussions

CURATION_TODO (RESOLVED): Keep the nuclear Q-nMT identity separate from generic nuclear microtubules and cytoplasmic Q-MT. Hidden- and ignored-inclusive identity, synonym and citation searches, plus a parsed identity scan, found no existing record. OAK GO alias searches and native GO definitions do not supply an exact Q-nMT term. GO:0099070 is broader; GO:0005880 is a constituent filament. The parallel monopolar nuclear array is not the antiparallel cytoplasmic S. pombe bundle or a bipolar mitotic spindle. OTHER denotes the whole array. Bare nuclear microtubule array is not adopted as an exact synonym.
CURATION_TODO (OPEN): Find exact whole-protein families for five label-only resident classes. Complete native InterPro matches were read for Bik1 P11709, Kar3 P17119, Bir1 P47134, Sli15 P38283 and Slk19 Q08581. Broad kinesin/BIR families and CAP-Gly, ARK-binding or TACC domains do not exactly identify these narrower classes. Label-only grounding is retained pending an exact authority entry.
CURATION_TODO (RESOLVED): Separate bundle composition from its nucleation site and attached chromosomal assemblies. The SPB nucleates the array but is not its containing structure. Tub4/Spc97/Spc72 mark the nucleation site. All six kinetochore subcomplexes have array-associated localization in 2013; Dad2 and Nuf2 mark attachments in 2024. These are retained as interacting chromosome-bound machinery rather than asserted stoichiometric building blocks of the microtubule bundle. Centromeric Cse4/chromosomes and the displaced nucleolus are likewise not bundle components. Slk19 is included because its own direct bundle-end localization and perturbation are documented.
CURATION_TODO (RESOLVED): Do not turn genetic requirements or expression into residence. Dynein and dynactin are detected on the cytoplasmic SPB face in 2013, not inside the nuclear array. Cik1 requirement, monopolin Mam1/Lrs4/Hrr25/Csm1 expression and deletion phenotypes, Spo13 effects, and tubulin-folding factors do not alone establish Q-nMT residence. Ipl1 activity is required early, but Ipl1 and Nbl1 were not detected in quiescence; the whole CPC is not imported from Bir1/Sli15 localization. Kip3 and She1 exit phenotypes are modeled as regulatory evidence, not stable-component evidence. She1 P38200 is distinct from the MYO4/SHE1 homonym P32492.
CURATION_TODO (RESOLVED): Keep assay sensitivity and individual deletion effects explicit. Kar3 was not detected in 2013 but later detected with 3GFP in 2024. Cin8 localization is faint and channel controls are shown in Figure 4 supplement 1B. Single BIM1 deletion permits stable bundles, whereas combinations expose redundancy. Tub3-specific requirements do not make Tub3 irreplaceable because Tub1 substitution restores stable bundles. Cin8 and Kip1 share a family but have distinct phenotypes; family-wide necessity is not tested. Short residual bundles after several deletions preclude an unqualified assembly-essential claim.
KNOWLEDGE_GAP (OPEN): Resolve stabilization without upgrading models into measured mechanisms. Nocodazole resistance, low tubulin turnover and stability after laser severing bound stability to these assays. A GTP cap inferred from Bim1 binding is not directly measured, and microtubule crosslinking mechanisms remain models. Survival/regrowth effects are supported but perturbations also act beyond this array. Proposed tubulin storage, a molecular SPB-separation checkpoint and homology with primary cilia are not asserted as demonstrated functions.
CURATION_TODO (RESOLVED): Avoid mixing biological dimensions, experimental expansion and control cells. Bundle length, thickness and maturation timing vary with condition; the 2024 Results and Discussion describe different approximate times for full stabilization. No universal size, count or schedule is imposed. Expansion microscopy expands the specimen, not the living bundle. Hosted Figure 3 supplement 1 is the unmodified mixed-modality figure: A and K include Q-nMT imaging; L is a proliferating-cell anaphase-spindle control. Cytoplasmic yellow background in A is explicitly described as nonspecific in Methods, not GFP localization.
CURATION_TODO (RESOLVED): Keep taxonomy, dataset coverage and licence claims bounded. Only S. cerevisiae is a canonical species. Most experiments use BY4741/BY4742 backgrounds, with stated S288C and W303 exceptions; reference-sequence examples are not exact-stock assertions. The adopted iModulonDB inventory has 28 datasets and no S. cerevisiae dataset; this is not a search of all omics repositories. Announced source-data spreadsheets were not inspected or promoted to curated datasets. Native PMC10963028.1 JATS and metadata agree on CC BY 4.0; the 2013 CC BY-NC-SA 3.0 figure is not hosted. No unverified TraitMech or Complex Portal link is added.

Evidence

DOI:10.1083/jcb.201306075 Laporte et al. (2013), PMID 24247429, native PMC3840927.1 Results, Discussion and relevant Methods: defining nuclear-array morphology, localization, perturbation and exit evidence.
DOI:10.7554/eLife.89958 Laporte et al. (2024), PMID 38527106, native PMC10963028.1 Results, Discussion and relevant Methods; Figure 3 supplement 1 and Figure 4 supplement 1 visually inspected.
GO:0099070 Non-obsolete static microtubule bundle term is broader than Q-nMT. Its Q-MT narrow synonyms concern the distinct fission-yeast cytoplasmic bundle.
GO:0005634 Native nucleus term supports nuclear compartment parthood.
GO:0015630 — microtubule cytoskeleton Native microtubule cytoskeleton term supports the encompassing framework.
GO:0005880 Native nuclear microtubule term describes the constituent polymers, not the whole multi-filament array.

Curation history

2026-10-05T16:36:00Z codex · CREATED_RECORD — Scaffolded by scripts/new_record.py
2026-10-05T16:38:33Z codex · EXPANDED_RECORD — Added ten component classes, eleven native-verified protein examples, bounded assembly/disassembly graphs, an inspected CC BY 4.0 figure, and explicit identity, component-boundary and evidence limitations.
2026-10-11T21:55:51Z codex · ADDRESS_SAVED_REVIEW — Addressed #2260, #2261: exposed preserved discussion explanations and graph scope in supported display fields; corrected Tub3 localization to Figure 2A and Figure 2 supplement 1A.

Source: data/structures/cytoskeleton/quiescent_nuclear_microtubule_bundle.yaml