The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.
You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.
We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.
We are interested in where in or outside the cell the gene product carries out its function.
We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.
Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.
Plan
We verified identity and nomenclature, gathered recent and foundational evidence on localization, stage, and molecular role, extracted application/disease-relevant mentions, synthesized a mechanistic narrative, and summarized key facts in a reference table for quick review.
| Aspect | Evidence/Details | Species/Context | Key source (with URL) | Publication date |
|---|---|---|---|---|
| Identity & family (C4orf43) | Identified as TMA16 (UniProt Q96EY4); member of the TMA16 family (Tma16/PF11176) and referred to as translation machinery-associated protein 16. | Human annotation / proteomics datasets | Paromov et al., Int. J. Mol. Sci.; DOI: https://doi.org/10.3390/ijms25031552 (mentions TMA16 / UniProt Q96EY4) (paromov2024theproteomicanalysis pages 1-2) | 26 Jan 2024 |
| Subcellular localization | Reported as nuclear/nucleolar and ribosome-associated; described as "nuclear-localized Tma16" in assembly-factor lists and observed in ribosome-associated particle datasets. | Yeast and human pre-ribosome studies; inferred nuclear → cytoplasmic pathway | Klingauf-Nerurkar et al., eLife; DOI: https://doi.org/10.7554/eLife.52474 (describes nuclear-localized Tma16) (purnima2020thegtpasenog1 pages 1-3) | 07 Jan 2020 |
| Stage of ribosome biogenesis | Implicated in late-stage 60S (pre-60S) maturation / export pathway (nucleolar → nuclear export → cytoplasmic maturation steps). | Pre-60S maturation pathway (eukaryotes) | Prattes et al., Nat. Struct. Mol. Biol.; DOI: https://doi.org/10.1038/s41594-022-00832-5 (context of pre-60S maturation and associated factors) (prattes2022visualizingmaturationfactor pages 7-8) | Sep 2022 |
| Particle association (pre-60S vs pre-40S) | Majority evidence supports association with pre-60S particles/export factors (eIF6, NMD3 listed alongside TMA16); some high-throughput datasets list TMA16 among ribosome-associated proteins (context can vary by study). | Predominantly pre-60S (assembly/export accessory lists) | Junod et al., iScience; DOI: https://doi.org/10.1016/j.isci.2023.107445 (lists eIF6, TMA16, LLPH, NMD3 in export/accessory context) (junod2023dynamicsofnuclear pages 6-10) | 18 Aug 2023 |
| Interacting factors / associations | Reported in contexts with Nog1/NOG2 replacement, Rlp24/Drg1-removal cascade, and export factors NMD3, eIF6, LLPH; also appears in translation-interaction screens (EIF4G2 studies). | Pre-60S export/maturation network; translation-interaction datasets | Klingauf-Nerurkar et al., eLife (Nog1/Rlp24 context) (purnima2020thegtpasenog1 pages 1-3); Meril et al., Life Sci. Alliance (EIF4G2 interactors include TMA16) (meril2024lossoffunctioncancerlinkedmutations pages 7-8) | 07 Jan 2020; Dec 2024 |
| Structural observations (cryo-EM) | Cryo-EM / structural summaries note limited/"weak density for Tma16 at the position reported in mammalian pre-60S" and that structural information in pre-60S context is lacking. | Cryo-EM of pre-60S particles (mammalian/yeast comparisons) | Prattes et al., Nat. Struct. Mol. Biol.; DOI: https://doi.org/10.1038/s41594-022-00832-5 (states weak density for Tma16) (prattes2022visualizingmaturationfactor pages 7-8) | Sep 2022 |
| Functional role | Inferred role as a ribosome-associated assembly/export adapter (replacement of export adapters like NOG2 reported in pathways); considered a ribosome-associated factor (RAF) rather than a catalytic enzyme. | Pre-60S export adapter / assembly factor (inference from genetics/biochemistry) | Klingauf-Nerurkar et al., eLife (Tma16 as export adapter in pathway; replacement of Nog2) (purnima2020thegtpasenog1 pages 1-3); Kanwal (thesis) noting "export adapter TMA16" (kanwal2023analysisofmultifunctional pages 67-71) | 07 Jan 2020; 2023 |
| Links to RQC / translation networks | Mentioned in broader translation and quality-control networks: yeast genetic screens and P-body regulation implicate TMA16 mRNA/protein in stress responses; listed among interactors in translation-initiation related studies (EIF4G2). | Yeast P-body / translation-stress context and human translation-interaction datasets | Loll-Krippleber et al., Nat. Commun. (TMA16 as ribosome-associated gene targeted by P-bodies) (lollkrippleber2017pbodyproteinsregulate pages 7-8); Meril et al., Life Sci. Alliance (EIF4G2 interactome mentions TMA16) (meril2024lossoffunctioncancerlinkedmutations pages 7-8) | 2017; Dec 2024 |
| Disease / biomarker / expression evidence | Detected in proteomic cancer "unfoldome" screens (identified but not integrated into interaction networks); appears in cancer-related translation interactomes but no established biomarker role yet. | Cancer proteomics (breast cancer unfoldome) and cancer mutation/interactome studies | Paromov et al., Int. J. Mol. Sci.; DOI: https://doi.org/10.3390/ijms25031552 (TMA16 detected but excluded from network) (paromov2024theproteomicanalysis pages 1-2); Meril et al., Life Sci. Alliance (EIF4G2 cancer study lists TMA16 among assembly factors) (meril2024lossoffunctioncancerlinkedmutations pages 7-8) | 26 Jan 2024; Dec 2024 |
| Cross-species / yeast evidence | Yeast Tma16 characterized in systematic ribosome-associated screens and functional assays; yeast data underpin many mechanistic inferences for the human ortholog. | Saccharomyces cerevisiae functional screens and pre-ribosome studies | Fleischer et al., Genes & Dev.; DOI: https://doi.org/10.1101/gad.1422006 (systematic ID of ribosome-associated proteins including TMA16/TMA family) (fleischer2006systematicidentificationand pages 7-8); Prattes & Klingauf-Nerurkar (pre-60S assembly studies referencing Tma16 in yeast) (prattes2022visualizingmaturationfactor pages 7-8, purnima2020thegtpasenog1 pages 1-3) | 2006; Sep 2022; Jan 2020 |
Table: Concise, evidence-backed summary of human TMA16 (UniProt Q96EY4) covering identity, localization, ribosome-stage association, interactions, structural notes, functional role, links to translation/RQC, disease proteomics, and cross-species (yeast) data with source URLs and publication dates.
Comprehensive research report: Human TMA16 (UniProt Q96EY4; gene symbol TMA16; alias C4orf43)
1) Key concepts and definitions (current understanding)
- Identity and family: TMA16 encodes translation machinery-associated protein 16, a conserved member of the TMA16 family (PF11176). In human proteomic resources, it is indexed as Q96EY4 (alias C4orf43). Recent large-scale proteomics mention TMA16 explicitly by UniProt ID (Q96EY4) in cancer unfoldome analyses, confirming protein identity in human datasets (though not placed in their interaction network) (https://doi.org/10.3390/ijms25031552; published 26 Jan 2024) (paromov2024theproteomicanalysis pages 1-2).
- Conceptual role: Across eukaryotes, Tma16 proteins are ribosome-associated factors (RAFs) implicated in large subunit (pre-60S) maturation/export steps rather than enzymatic catalysis. Foundational yeast work systematically identified TMA proteins as ribosome-associated and affecting translation phenotypes, establishing a conserved functional class to which Tma16 belongs (https://doi.org/10.1101/gad.1422006; 22 May 2006) (fleischer2006systematicidentificationand pages 7-8).
2) Recent developments and latest research (2023–2024 priority)
- Association with pre-60S export/maturation modules in live cells: High-speed single-molecule microscopy of human pre-ribosomal subunits quantified nuclear export and collated accessory proteins, listing eIF6, TMA16, LLPH, and NMD3 among factors associated with pre-60S export/maturation, supporting a role for human TMA16 in late pre-60S biology (https://doi.org/10.1016/j.isci.2023.107445; 18 Aug 2023) (junod2023dynamicsofnuclear pages 6-10).
- Structural context from cryo-EM: In structural studies visualizing Drg1-mediated extraction of Rlp24 from pre-60S particles, authors note “weak density for Tma16 at the position reported in mammalian pre-60S,” and broadly that structural information for some pre-60S assembly factors including Tma16 remains limited. This places Tma16 at a defined site on mammalian pre-60S but underscores incomplete structural resolution (https://doi.org/10.1038/s41594-022-00832-5; 12 Sep 2022) (prattes2022visualizingmaturationfactor pages 7-8).
- Network placement with translation initiation machinery: An analysis of cancer-linked EIF4G2 (a non-canonical translation initiation factor) reports newly identified interacting proteins that include ribosome assembly factors such as TMA16, situating TMA16 within broader translation-initiation/assembly interaction landscapes in human cells (https://doi.org/10.26508/lsa.202302338; 2 Dec 2024) (meril2024lossoffunctioncancerlinkedmutations pages 7-8).
- Cancer proteomics context: A 2024 proteomics study of breast cancer “unfoldome” (IDP/IDPR-enriched proteome) identifies TMA16 by UniProt ID but notes it was not included in the resulting interactivity network, indicating detection without strong network integration in that dataset (https://doi.org/10.3390/ijms25031552; 26 Jan 2024) (paromov2024theproteomicanalysis pages 1-2).
3) Current applications and real-world implementations
- Ribosome biogenesis/export biology: Live-cell imaging quantifies pre-60S export times (13 ± 1 ms) and pre-40S (9 ± 1 ms) through nuclear pore complexes and lists TMA16 among pre-60S accessory/export factors. While these statistics describe subunit dynamics, they contextualize TMA16’s likely stage and compartment of action during pre-60S nuclear export and early cytoplasmic maturation (https://doi.org/10.1016/j.isci.2023.107445; 18 Aug 2023) (junod2023dynamicsofnuclear pages 6-10).
- Translational networks and disease research: EIF4G2-focused human studies that list TMA16 among assembly factors map potential interfaces between translation initiation and ribosome assembly, relevant to oncology-focused translation control research (https://doi.org/10.26508/lsa.202302338; 2 Dec 2024) (meril2024lossoffunctioncancerlinkedmutations pages 7-8).
4) Expert opinions and analysis from authoritative sources
- Ribosome maturation context: Pre-60S cytoplasmic maturation, governed by the AAA-ATPase Drg1 and the GTPase Nog1/NOG2 pathways, has been dissected in detail. Although specific direct biochemistry for human TMA16 remains sparse, authoritative work notes Tma16 as a nuclear-localized assembly factor in pre-60S maturation lists and that structural information for Tma16 on pre-60S is lacking, consistent with an accessory/adapter function rather than a catalytic role (eLife perspective on Nog1 and maturation coordination, 7 Jan 2020: https://doi.org/10.7554/eLife.52474) (purnima2020thegtpasenog1 pages 1-3); structural analysis of Drg1 action and mention of Tma16 placement/density, 12 Sep 2022: https://doi.org/10.1038/s41594-022-00832-5 (prattes2022visualizingmaturationfactor pages 7-8).
- Yeast functional screens: Systematic identification of ribosome-associated proteins (including TMA family members) and translation phenotyping in yeast provide a comparative framework supporting conserved ribosome-association for Tma16 homologs (https://doi.org/10.1101/gad.1422006; 22 May 2006) (fleischer2006systematicidentificationand pages 7-8).
5) Relevant statistics and data from recent studies
- Pre-ribosomal subunit export kinetics: In live human cells, successful nuclear export time for pre-60S is 13 ± 1 ms and for pre-40S is 9 ± 1 ms (single-molecule measurements). These data frame the time window in which pre-60S export adapters/accessories (including TMA16, eIF6, NMD3, LLPH) act (https://doi.org/10.1016/j.isci.2023.107445; 18 Aug 2023) (junod2023dynamicsofnuclear pages 6-10).
- Cancer proteomics coverage: The 2024 breast cancer unfoldome analysis reports 2,271 protein groups in unfoldome fractions, with 148 intrinsically disordered proteins (IDPs) differentially expressed. TMA16 (Q96EY4) is detected but excluded from the final interaction network, indicating presence yet uncertain network connectivity in that dataset (https://doi.org/10.3390/ijms25031552; 26 Jan 2024) (paromov2024theproteomicanalysis pages 1-2).
Functional annotation and mechanistic model
- Subcellular localization: Evidence aggregates to a predominantly nuclear/pre-60S association, consistent with a role in late nucleoplasmic steps and nuclear export of the large subunit. Tma16 is referenced as nuclear-localized in pre-60S assembly factor discussions (https://doi.org/10.7554/eLife.52474; 7 Jan 2020) (purnima2020thegtpasenog1 pages 1-3) and appears in the pre-60S export accessory list in human live-cell work (https://doi.org/10.1016/j.isci.2023.107445; 18 Aug 2023) (junod2023dynamicsofnuclear pages 6-10).
- Stage of ribosome biogenesis: The linkage to pre-60S export/maturation steps (alongside eIF6, NMD3) places TMA16 late in the large subunit assembly trajectory, near or during nuclear export and early cytoplasmic maturation (https://doi.org/10.1016/j.isci.2023.107445; 18 Aug 2023) (junod2023dynamicsofnuclear pages 6-10). Structural work on Drg1-mediated Rlp24 removal and Nog1-dependent steps provides the mechanistic context into which Tma16 is placed, albeit with limited direct structural detail (https://doi.org/10.1038/s41594-022-00832-5; 12 Sep 2022) (prattes2022visualizingmaturationfactor pages 7-8); (https://doi.org/10.7554/eLife.52474; 7 Jan 2020) (purnima2020thegtpasenog1 pages 1-3).
- Molecular function: The collective evidence supports classification as a ribosome-associated factor (RAF) or export adapter in the pre-60S pathway, not as an enzyme or transporter. It likely functions as an accessory component facilitating ribosomal subunit export or maturation checkpoint transitions, consistent with its co-listing among eIF6 and NMD3 (https://doi.org/10.1016/j.isci.2023.107445; 18 Aug 2023) (junod2023dynamicsofnuclear pages 6-10) and its mention as a nuclear-localized, structurally under-characterized assembly factor (https://doi.org/10.1038/s41594-022-00832-5; 12 Sep 2022) (prattes2022visualizingmaturationfactor pages 7-8); (https://doi.org/10.7554/eLife.52474; 7 Jan 2020) (purnima2020thegtpasenog1 pages 1-3).
- Particle association and interactions: Human evidence favors pre-60S association (eIF6, NMD3, LLPH co-mention with TMA16) (https://doi.org/10.1016/j.isci.2023.107445; 18 Aug 2023) (junod2023dynamicsofnuclear pages 6-10). Independent analyses of translation initiation networks (EIF4G2) also list TMA16 among assembly factors, implying connectivity to translation initiation machinery (https://doi.org/10.26508/lsa.202302338; 2 Dec 2024) (meril2024lossoffunctioncancerlinkedmutations pages 7-8). Foundational yeast studies embed Tma16 within ribosome-associated proteomes (https://doi.org/10.1101/gad.1422006; 22 May 2006) (fleischer2006systematicidentificationand pages 7-8). Direct binary interactions for human TMA16 remain sparsely resolved in the cited works.
- Structural observations: Cryo-EM studies report only weak density for Tma16 at the mammalian pre-60S site and note a general lack of structural information for Tma16 on pre-60S, indicating that its exact binding mode and interfaces remain to be precisely defined (https://doi.org/10.1038/s41594-022-00832-5; 12 Sep 2022) (prattes2022visualizingmaturationfactor pages 7-8). This cautions against over-specifying binding partners without further primary structural evidence.
- RQC/translation stress networks: While direct RQC assignment for TMA16 is not established in the human-focused sources above, yeast replication stress work implicates TMA16 (mRNA) among P-body-regulated targets, and authors annotate TMA16 and RRS1 as ribosome-associated genes affected under stress, linking TMA16 to mRNA fate pathways under genotoxic stress (https://doi.org/10.1038/s41467-017-00632-2; 22 Sep 2017) (lollkrippleber2017pbodyproteinsregulate pages 7-8). This supports a model where TMA16 expression may be tuned by RNA granule pathways under stress, indirectly connecting it to translation quality control.
Disease associations and translational relevance
- Cancer/biomarker context: Current human data show detection of TMA16 in cancer proteome fractions (unfoldome) but do not yet substantiate a robust biomarker or therapeutic association; it was not included in the interactome network of that 2024 study (https://doi.org/10.3390/ijms25031552; 26 Jan 2024) (paromov2024theproteomicanalysis pages 1-2). The EIF4G2 cancer study providing interaction landscape mentions TMA16 among assembly factors, suggesting indirect relevance to translation alterations in tumors, but without TMA16-focused functional oncology data (https://doi.org/10.26508/lsa.202302338; 2 Dec 2024) (meril2024lossoffunctioncancerlinkedmutations pages 7-8). Thus, disease linkage remains preliminary and inferential.
Limitations and open questions
- Direct biochemical function and high-resolution structure for human TMA16 on pre-60S remain incompletely defined; cryo-EM studies note weak or unassigned density and lack of detailed positioning. Additional proteomics, interaction mapping, and structural work (focused on human pre-60S particles) will be needed to firmly place TMA16 within specific export or maturation checkpoints (https://doi.org/10.1038/s41594-022-00832-5; 12 Sep 2022) (prattes2022visualizingmaturationfactor pages 7-8); (https://doi.org/10.7554/eLife.52474; 7 Jan 2020) (purnima2020thegtpasenog1 pages 1-3).
Mandatory verification summary
- Gene symbol and protein match: TMA16 (human) corresponds to translation machinery-associated protein 16, UniProt Q96EY4, consistent with database and recent proteomics mentions (https://doi.org/10.3390/ijms25031552; 26 Jan 2024) (paromov2024theproteomicanalysis pages 1-2).
- Organism: Homo sapiens; all primary recent data cited for identity and accessory lists are human studies (iScience 2023; Life Sci Alliance 2024; IJMS 2024) (junod2023dynamicsofnuclear pages 6-10, meril2024lossoffunctioncancerlinkedmutations pages 7-8, paromov2024theproteomicanalysis pages 1-2).
- Domains/family alignment: Belongs to the TMA16 family; literature consistently refers to Tma16 as a ribosome-associated factor in eukaryotes; no conflict detected (fleischer2006systematicidentificationand pages 7-8, purnima2020thegtpasenog1 pages 1-3).
- Ambiguity check: No conflicting gene/protein with the TMA16 symbol was used; instances referring to yeast Tma16 are used only for comparative inference and pathway context.
References (URLs and dates)
- Paromov V et al. The Proteomic Analysis of Cancer-Related Alterations in the Human Unfoldome. Int J Mol Sci. Published 26 Jan 2024. https://doi.org/10.3390/ijms25031552 (paromov2024theproteomicanalysis pages 1-2).
- Junod SL et al. Dynamics of nuclear export of pre-ribosomal subunits… iScience. Published 18 Aug 2023. https://doi.org/10.1016/j.isci.2023.107445 (junod2023dynamicsofnuclear pages 6-10).
- Prattes M et al. Visualizing maturation factor extraction… Nat Struct Mol Biol. Published 12 Sep 2022. https://doi.org/10.1038/s41594-022-00832-5 (prattes2022visualizingmaturationfactor pages 7-8, prattes2022visualizingmaturationfactor pages 10-11).
- Klingauf-Nerurkar P et al. The GTPase Nog1 co-ordinates… eLife. Published 7 Jan 2020. https://doi.org/10.7554/eLife.52474 (purnima2020thegtpasenog1 pages 1-3).
- Meril S et al. Loss-of-function cancer-linked mutations in EIF4G2… Life Sci Alliance. Published 2 Dec 2024. https://doi.org/10.26508/lsa.202302338 (meril2024lossoffunctioncancerlinkedmutations pages 7-8).
- Loll-Krippleber R, Brown GW. P-body proteins regulate transcriptional rewiring… Nat Commun. Published 22 Sep 2017. https://doi.org/10.1038/s41467-017-00632-2 (lollkrippleber2017pbodyproteinsregulate pages 7-8).
- Fleischer TC et al. Systematic identification and functional screens… Genes Dev. Published 22 May 2006. https://doi.org/10.1101/gad.1422006 (fleischer2006systematicidentificationand pages 7-8).
Citations: Paromov 2024 (paromov2024theproteomicanalysis pages 1-2); Junod 2023 (junod2023dynamicsofnuclear pages 6-10); Prattes 2022 (prattes2022visualizingmaturationfactor pages 7-8, prattes2022visualizingmaturationfactor pages 10-11); Klingauf-Nerurkar 2020 (purnima2020thegtpasenog1 pages 1-3); Meril 2024 (meril2024lossoffunctioncancerlinkedmutations pages 7-8); Loll-Krippleber 2017 (lollkrippleber2017pbodyproteinsregulate pages 7-8); Fleischer 2006 (fleischer2006systematicidentificationand pages 7-8).
References
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