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Sharma VS, Fossati A, Ciuffa R, Buljan M, Williams EG, Chen Z, Shao W, Pedrioli PGA, Purcell AW, Martínez MR, Song J, Manica M, Aebersold R, Li C. PCfun: a hybrid computational framework for systematic characterization of protein complex function. Brief Bioinform 2022; 23:6611913. [PMID: 35724564 PMCID: PMC9310514 DOI: 10.1093/bib/bbac239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/05/2022] [Accepted: 05/21/2022] [Indexed: 11/14/2022] Open
Abstract
In molecular biology, it is a general assumption that the ensemble of expressed molecules, their activities and interactions determine biological function, cellular states and phenotypes. Stable protein complexes—or macromolecular machines—are, in turn, the key functional entities mediating and modulating most biological processes. Although identifying protein complexes and their subunit composition can now be done inexpensively and at scale, determining their function remains challenging and labor intensive. This study describes Protein Complex Function predictor (PCfun), the first computational framework for the systematic annotation of protein complex functions using Gene Ontology (GO) terms. PCfun is built upon a word embedding using natural language processing techniques based on 1 million open access PubMed Central articles. Specifically, PCfun leverages two approaches for accurately identifying protein complex function, including: (i) an unsupervised approach that obtains the nearest neighbor (NN) GO term word vectors for a protein complex query vector and (ii) a supervised approach using Random Forest (RF) models trained specifically for recovering the GO terms of protein complex queries described in the CORUM protein complex database. PCfun consolidates both approaches by performing a hypergeometric statistical test to enrich the top NN GO terms within the child terms of the GO terms predicted by the RF models. The documentation and implementation of the PCfun package are available at https://github.com/sharmavaruns/PCfun. We anticipate that PCfun will serve as a useful tool and novel paradigm for the large-scale characterization of protein complex function.
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Affiliation(s)
- Varun S Sharma
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland.,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Andrea Fossati
- Quantitative Biosciences Institute (QBI) and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Rodolfo Ciuffa
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland
| | - Marija Buljan
- Empa - Swiss Federal Laboratories for Materials Science and Technology, St. Gallen, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Evan G Williams
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette Luxembourg
| | - Zhen Chen
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450046, China
| | - Wenguang Shao
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland
| | - Patrick G A Pedrioli
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland
| | - Anthony W Purcell
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | | | - Jiangning Song
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia.,Monash Data Futures Institute, Monash University, Melbourne, VIC 3800, Australia
| | | | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland.,Faculty of Science, University of Zurich, Switzerland
| | - Chen Li
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland.,Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
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Nakabayashi Y, Seki M. Transcription destabilizes centromere function. Biochem Biophys Res Commun 2022; 586:150-156. [PMID: 34844121 DOI: 10.1016/j.bbrc.2021.11.077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 11/22/2021] [Indexed: 12/26/2022]
Abstract
Bi-oriented attachment of microtubules to the centromere is a pre-requisite for faithful chromosome segregation during mitosis. Budding yeast have point centromeres containing the cis-element proteins CDE-I, -II, and -III, which interact with trans-acting factors such as Cbf1, Cse4, and Ndc10. Our previous genetic screens, using a comprehensive library of histone point mutants, revealed that the TBS-I, -II, and -III regions of nucleosomes are required for faithful chromosome segregation. In TBS-III deficient cells, peri-centromeric nucleosomes containing the H2A.Z homolog Htz1 are lacking, however, it is unclear why chromosome segregation is defective in these cells. Here, we show that, in cells lacking TBS-III, both chromatin binding at the centromere and the total amount of some of the centromere proteins are reduced, and transcription through the centromere is up-regulated during M-phase. Moreover, the chromatin binding of Cse4, Mif2, Cbf1, Ndc10, and Scm3 was reduced upon ectopic transcription through the centromere in wild-type cells. These results suggest that transcription through the centromere displaces key centromere proteins and, consequently, destabilizes the interaction between centromeres and microtubules, leading to defective chromosome segregation. The identification of new roles for histone binding residues in TBS-III will shed new light on nucleosome function during chromosome segregation.
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Affiliation(s)
- Yu Nakabayashi
- Division of Biochemistry, Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai, Miyagi, 981-8558, Japan
| | - Masayuki Seki
- Division of Biochemistry, Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai, Miyagi, 981-8558, Japan.
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Kitagawa S, Kusakabe M, Takahashi D, Narimiya T, Nakabayashi Y, Seki M, Horigome C, Harata M. Analysis of the molecular evolution of histone variant H2A.Z using a linker-mediated complex strategy and yeast genetic complementation. Biosci Biotechnol Biochem 2021; 86:104-108. [PMID: 34718407 DOI: 10.1093/bbb/zbab190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 10/25/2021] [Indexed: 11/12/2022]
Abstract
The histone variant H2A.Z is deposited into chromatin by specific machinery and is required for genome functions. Using a linker-mediated complex strategy combined with yeast genetic complementation, we demonstrate evolutionary conservation of H2A.Z together with its chromatin incorporation and functions. This approach is applicable to the evolutionary analyses of proteins that form complexes with interactors.
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Affiliation(s)
- Saho Kitagawa
- Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai, Miyagi, Japan
| | - Masayuki Kusakabe
- Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai, Miyagi, Japan
| | - Daisuke Takahashi
- Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai, Miyagi, Japan
| | - Takumi Narimiya
- Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai, Miyagi, Japan
| | - Yu Nakabayashi
- Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, Aoba-ku, Sendai, Miyagi, Japan
| | - Masayuki Seki
- Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, Aoba-ku, Sendai, Miyagi, Japan
| | - Chihiro Horigome
- Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai, Miyagi, Japan
| | - Masahiko Harata
- Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai, Miyagi, Japan
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Choi HI, Hwang SW, Kim J, Park B, Jin E, Choi IG, Sim SJ. Augmented CO 2 tolerance by expressing a single H +-pump enables microalgal valorization of industrial flue gas. Nat Commun 2021; 12:6049. [PMID: 34663809 PMCID: PMC8523702 DOI: 10.1038/s41467-021-26325-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 10/01/2021] [Indexed: 12/02/2022] Open
Abstract
Microalgae can accumulate various carbon-neutral products, but their real-world applications are hindered by their CO2 susceptibility. Herein, the transcriptomic changes in a model microalga, Chlamydomonas reinhardtii, in a high-CO2 milieu (20%) are evaluated. The primary toxicity mechanism consists of aberrantly low expression of plasma membrane H+-ATPases (PMAs) accompanied by intracellular acidification. Our results demonstrate that the expression of a universally expressible PMA in wild-type strains makes them capable of not only thriving in acidity levels that they usually cannot survive but also exhibiting 3.2-fold increased photoautotrophic production against high CO2 via maintenance of a higher cytoplasmic pH. A proof-of-concept experiment involving cultivation with toxic flue gas (13 vol% CO2, 20 ppm NOX, and 32 ppm SOX) shows that the production of CO2-based bioproducts by the strain is doubled compared with that by the wild-type, implying that this strategy potentially enables the microalgal valorization of CO2 in industrial exhaust.
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Affiliation(s)
- Hong Il Choi
- Department of Chemical and Biological Engineering, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Sung-Won Hwang
- Department of Chemical and Biological Engineering, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Jongrae Kim
- Department of Life Science, Hanyang University, 206, Wangsimni-ro, Seongbuk-gu, Seoul, 04763, Republic of Korea
| | - Byeonghyeok Park
- Department of Biotechnology, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - EonSeon Jin
- Department of Life Science, Hanyang University, 206, Wangsimni-ro, Seongbuk-gu, Seoul, 04763, Republic of Korea
| | - In-Geol Choi
- Department of Biotechnology, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Sang Jun Sim
- Department of Chemical and Biological Engineering, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea.
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An improved functional analysis of linker-mediated complex (iFALC) strategy. Biochem Biophys Res Commun 2020; 526:1164-1169. [PMID: 32327258 DOI: 10.1016/j.bbrc.2020.04.039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 04/10/2020] [Indexed: 11/20/2022]
Abstract
The functional analysis of linker-mediated complex (FALC) strategy that facilitates functional analysis of a common subunit of multi-subunit protein complexes in cells constitutes three steps; (1) a common subunit is fused to a specific subunit via recombinant DNA, (2) mutation is introduced into a portion of the common subunit of the fused protein, and (3) the mutational effect on the fused protein is evaluated by transformation and analysis of multiple appropriate gene knockout yeast strains. Conceptually, the FALC strategy is applicable to any common subunit of multi-subunit protein complexes in any cell type. However, the proximity of two subunits to fuse, preparation of multiple gene knockout cells, and utilization of yeast cells can together prevent the practical and broad usage of the FALC strategy for analyzing all multi-subunit complexes in all cell types. In this study, we analyzed histone H2B as a common subunit of histone H2A/H2B and histone variant H2A.Z/H2B dimers. The FALC strategy was improved in three ways; (i) a long linker (up to 300 amino acids) was used to fuse H2B with H2A.Z in yeast cells, (ii) the effects of the fused H2B-H2A.Z harboring mutation in the H2B portion was evaluated in H2A.Z knockout yeast strains and it was not essential to knockout two copies of H2B genes, and (iii) this occurred even in vertebrate cells possessing a dozen H2B genes. This improved FALC (iFALC) strategy reveals that vertebrate H2B-D68, corresponding to yeast H2B-D71, is critical for chromatin binding of the H2A.Z/H2B dimer, and this is evolutionarily conserved.
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MacroH2A1 chromatin specification requires its docking domain and acetylation of H2B lysine 20. Nat Commun 2018; 9:5143. [PMID: 30510186 PMCID: PMC6277393 DOI: 10.1038/s41467-018-07189-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 10/13/2018] [Indexed: 12/23/2022] Open
Abstract
The histone variant macroH2A1 localizes to two functionally distinct chromatin subtypes marked by either H3K27me3 or H2B acetylations, where it is thought to directly regulate transcription. The recent finding, that macroH2A1 regulates mitochondrial respiration by globally dampening PARP activity, requires the field to re-evaluate which functions of macroH2A1 are due to global effects on cellular metabolism and which are direct effects determined by macroH2A1 chromatin localization. Here, we demonstrate macroH2A1 incorporation into H2B-acetylated chromatin requires a feature in its histone-fold domain, distinguishing this process from incorporation into H3K27me3-containing chromatin in which multiple features of macroH2A1 are sufficient for targeting. In addition, we identify H2BK20 acetylation as a critical modification required to target macroH2A1 to H2B-acetylated chromatin. Our findings have allowed us to definitively establish that macroH2A1's regulation of an important transcriptional program, the senescence-associated secretory phenotype (SASP), requires its accurate genomic localization.
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Identification of a histone family gene signature for predicting the prognosis of cervical cancer patients. Sci Rep 2017; 7:16495. [PMID: 29184082 PMCID: PMC5705706 DOI: 10.1038/s41598-017-16472-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 11/13/2017] [Indexed: 01/01/2023] Open
Abstract
Heterogeneity in terms of tumor characteristics, prognosis, and survival among cancer patients is an unsolved issue. Here, we systematically analyzed the aberrant expression patterns of cervical cancer using RNA-Seq data from The Cancer Genome Atlas (TCGA). We incorporated gene profiling, molecular signatures, functional and pathway information with gene set enrichment and protein-protein interaction (PPI) network analysis, to identify sub-networks of genes. Those identified genes relating to DNA replication and DNA repair-mediated signaling pathways associated with systemic lupus erythematosus (SLE). Next, we combined cross-validated prognostic scores to build an integrated prognostic model for survival prediction. The combined approach revealed that the DNA repair-mediated including the functional interaction module of 18 histone genes (Histone cluster 1 H2A, B and H4), were significantly correlated with the survival rate. Furthermore, five of these histone genes were highly expressed in three cervical cancer cohorts from the Oncomine database. Comparison of high and low histone variant-expressing human cervical cancer cell lines revealed different responses to DNA damage, suggesting protective functions of histone genes against DNA damage. Collectively, we provide evidence that two SLE-associated gene sets (HIST1H2BD and HIST1H2BJ; and HIST1H2BD, HIST1H2BJ, HIST1H2BH, HIST1H2AM and HIST1H4K) can be used as prognostic factors for survival prediction among cervical cancer patients.
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