1
|
Mishra AK, Ye T, Banday S, Thakare RP, Su CTT, Pham NNH, Ali A, Kulshreshtha A, Chowdhury SR, Simone TM, Hu K, Zhu LJ, Eisenhaber B, Deibler SK, Simin K, Thompson PR, Kelliher MA, Eisenhaber F, Malonia SK, Green MR. Targeting the GPI transamidase subunit GPAA1 abrogates the CD24 immune checkpoint in ovarian cancer. Cell Rep 2024; 43:114041. [PMID: 38573857 DOI: 10.1016/j.celrep.2024.114041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/25/2024] [Accepted: 03/19/2024] [Indexed: 04/06/2024] Open
Abstract
CD24 is frequently overexpressed in ovarian cancer and promotes immune evasion by interacting with its receptor Siglec10, present on tumor-associated macrophages, providing a "don't eat me" signal that prevents targeting and phagocytosis by macrophages. Factors promoting CD24 expression could represent novel immunotherapeutic targets for ovarian cancer. Here, using a genome-wide CRISPR knockout screen, we identify GPAA1 (glycosylphosphatidylinositol anchor attachment 1), a factor that catalyzes the attachment of a glycosylphosphatidylinositol (GPI) lipid anchor to substrate proteins, as a positive regulator of CD24 cell surface expression. Genetic ablation of GPAA1 abolishes CD24 cell surface expression, enhances macrophage-mediated phagocytosis, and inhibits ovarian tumor growth in mice. GPAA1 shares structural similarities with aminopeptidases. Consequently, we show that bestatin, a clinically advanced aminopeptidase inhibitor, binds to GPAA1 and blocks GPI attachment, resulting in reduced CD24 cell surface expression, increased macrophage-mediated phagocytosis, and suppressed growth of ovarian tumors. Our study highlights the potential of targeting GPAA1 as an immunotherapeutic approach for CD24+ ovarian cancers.
Collapse
Affiliation(s)
- Alok K Mishra
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.
| | - Tianyi Ye
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Shahid Banday
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Ritesh P Thakare
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Chinh Tran-To Su
- Bioinformatics Institute (BII), Agency for Science, Technology, and Research (A(∗)STAR), 30 Biopolis Street, Matrix, #07-01, Singapore 138671, Singapore
| | - Ngoc N H Pham
- Faculty of Biology and Biotechnology, University of Science, Vietnam National University, 227 Nguyen Van Cu Street, District 5, Ho Chi Minh City, Vietnam
| | - Amjad Ali
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Ankur Kulshreshtha
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Shreya Roy Chowdhury
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Tessa M Simone
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Kai Hu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Lihua Julie Zhu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; Program in Molecular Medicine and Department of Genomics and Computational Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Birgit Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology, and Research (A(∗)STAR), 30 Biopolis Street, Matrix, #07-01, Singapore 138671, Singapore; Lausitz Advanced Scientific Applications (LASA) gGmbH, Straße der Einheit 2-24, 02943 Weißwasser, Germany
| | - Sara K Deibler
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Karl Simin
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Paul R Thompson
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Michelle A Kelliher
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Frank Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology, and Research (A(∗)STAR), 30 Biopolis Street, Matrix, #07-01, Singapore 138671, Singapore; Lausitz Advanced Scientific Applications (LASA) gGmbH, Straße der Einheit 2-24, 02943 Weißwasser, Germany; School of Biological Sciences, Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore 637551, Singapore.
| | - Sunil K Malonia
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.
| | - Michael R Green
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| |
Collapse
|
2
|
Iyer NR, Chan SP, Liew OW, Chong JPC, Bryant JA, Le TT, Chandramouli C, Cozzone PJ, Eisenhaber F, Foo R, Richards AM, Lam CSP, Ugander M, Chin CWL. Global longitudinal strain and plasma biomarkers for prognosis in heart failure complicated by diabetes: a prospective observational study. BMC Cardiovasc Disord 2024; 24:141. [PMID: 38443793 PMCID: PMC10913625 DOI: 10.1186/s12872-024-03810-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 02/22/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND Heart failure (HF) and diabetes are associated with increased incidence and worse prognosis of each other. The prognostic value of global longitudinal strain (GLS) measured by cardiovascular magnetic resonance (CMR) has not been established in HF patients with diabetes. METHODS In this prospective, observational study, consecutive patients (n = 315) with HF underwent CMR at 3T, including GLS, late gadolinium enhancement (LGE), native T1, and extracellular volume fraction (ECV) mapping. Plasma biomarker concentrations were measured including: N-terminal pro B-type natriuretic peptide(NT-proBNP), high-sensitivity troponin T(hs-TnT), growth differentiation factor 15(GDF-15), soluble ST2(sST2), and galectin 3(Gal-3). The primary outcome was a composite of all-cause mortality or HF hospitalisation. RESULTS Compared to those without diabetes (n = 156), the diabetes group (n = 159) had a higher LGE prevalence (76 vs. 60%, p < 0.05), higher T1 (1285±42 vs. 1269±42ms, p < 0.001), and higher ECV (30.5±3.5 vs. 28.8±4.1%, p < 0.001). The diabetes group had higher NT-pro-BNP, hs-TnT, GDF-15, sST2, and Gal-3. Diabetes conferred worse prognosis (hazard ratio (HR) 2.33 [95% confidence interval (CI) 1.43-3.79], p < 0.001). In multivariable Cox regression analysis including clinical markers and plasma biomarkers, sST2 alone remained independently associated with the primary outcome (HR per 1 ng/mL 1.04 [95% CI 1.02-1.07], p = 0.001). In multivariable Cox regression models in the diabetes group, both GLS and sST2 remained prognostic (GLS: HR 1.12 [95% CI 1.03-1.21], p = 0.01; sST2: HR per 1 ng/mL 1.03 [95% CI 1.00-1.06], p = 0.02). CONCLUSIONS Compared to HF patients without diabetes, those with diabetes have worse plasma and CMR markers of fibrosis and a more adverse prognosis. GLS by CMR is a powerful and independent prognostic marker in HF patients with diabetes.
Collapse
Affiliation(s)
- Nithin R Iyer
- National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore, Singapore
- Kolling Institute, Royal North Shore Hospital, University of Sydney, Sydney, Australia
| | - Siew-Pang Chan
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Oi Wah Liew
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jenny P C Chong
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jennifer A Bryant
- National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore, Singapore
| | - Thu-Thao Le
- National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore, Singapore
- Cardiovascular Sciences ACP, Duke-NUS Medical School, Singapore, Singapore
| | - Chanchal Chandramouli
- National Heart Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Patrick J Cozzone
- Agency for Science, Technology and Research, Singapore Bioimaging Consortium, Singapore, Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute, Agency for Science, Technology and Research, Singapore, Singapore
- LASA - Lausitz Advanced Scientific Applications gGmbH, Weißwasser, Germany
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Roger Foo
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Agency for Science, Technology and Research, Genome Institute of Singapore, Singapore, Singapore
| | - A Mark Richards
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Christchurch Heart Institute, University of Otago, Christchurch, New Zealand
| | - Carolyn S P Lam
- National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore, Singapore
- National Heart Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
- University Medical Centre Groningen, Groningen, The Netherlands
| | - Martin Ugander
- Kolling Institute, Royal North Shore Hospital, University of Sydney, Sydney, Australia
- Department of Clinical Physiology, Karolinska University Hospital, and Karolinska Institutet, Stockholm, Sweden
| | - Calvin W-L Chin
- Cardiovascular Sciences ACP, Duke-NUS Medical School, Singapore, Singapore.
- National Heart Centre Singapore, Singapore, Singapore.
| |
Collapse
|
3
|
Alfatah M, Zhang Y, Naaz A, Cheng TYN, Eisenhaber F. PICLS with human cells is the first high throughput screening method for identifying novel compounds that extend lifespan. Biol Direct 2024; 19:8. [PMID: 38254217 PMCID: PMC10804585 DOI: 10.1186/s13062-024-00455-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 01/18/2024] [Indexed: 01/24/2024] Open
Abstract
Gerontology research on anti-aging interventions with drugs could be an answer to age-related diseases, aiming at closing the gap between lifespan and healthspan. Here, we present two methods for assaying chronological lifespan in human cells: (1) a version of the classical outgrowth assay with quantitative assessment of surviving cells and (2) a version of the PICLS method (propidium iodide fluorescent-based measurement of cell death). Both methods are fast, simple to conduct, cost-effective, produce quantitative data for further analysis and can be used with diverse human cell lines. Whereas the first method is ideal for validation and testing the post-intervention reproductive potential of surviving cells, the second method has true high-throughput screening potential. The new technologies were validated with known anti-aging compounds (2,5-anhydro-D-mannitol and rapamycin). Using the high-throughput screening method, we screened a library of 162 chemical entities and identified three compounds that extend the longevity of human cells.
Collapse
Affiliation(s)
- Mohammad Alfatah
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Matrix #07-01, Singapore, 138671, Republic of Singapore.
| | - Yizhong Zhang
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Matrix #07-01, Singapore, 138671, Republic of Singapore
| | - Arshia Naaz
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome #02-01, Singapore, 138672, Republic of Singapore
| | - Trishia Yi Ning Cheng
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Matrix #07-01, Singapore, 138671, Republic of Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Matrix #07-01, Singapore, 138671, Republic of Singapore
- LASA - Lausitz Advanced Scientific Applications gGmbH, Straße der Einheit 2-24, 02943, Weißwasser, Federal Republic of Germany
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), Singapore, 637551, Republic of Singapore
| |
Collapse
|
4
|
Batagov A, Dalan R, Wu A, Lai W, Tan CS, Eisenhaber F. Generalized metabolic flux analysis framework provides mechanism-based predictions of ophthalmic complications in type 2 diabetes patients. Health Inf Sci Syst 2023; 11:18. [PMID: 37008895 PMCID: PMC10060506 DOI: 10.1007/s13755-023-00218-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 02/19/2023] [Indexed: 03/31/2023] Open
Abstract
Chronic metabolic diseases arise from changes in metabolic fluxes through biomolecular pathways and gene networks accumulated over the lifetime of an individual. While clinical and biochemical profiles present just real-time snapshots of the patients' health, efficient computation models of the pathological disturbance of biomolecular processes are required to achieve individualized mechanistic insights into disease progression. Here, we describe the Generalized metabolic flux analysis (GMFA) for addressing this gap. Suitably grouping individual metabolites/fluxes into pools simplifies the analysis of the resulting more coarse-grain network. We also map non-metabolic clinical modalities onto the network with additional edges. Instead of using the time coordinate, the system status (metabolite concentrations and fluxes) is quantified as function of a generalized extent variable (a coordinate in the space of generalized metabolites) that represents the system's coordinate along its evolution path and evaluates the degree of change between any two states on that path. We applied GMFA to analyze Type 2 Diabetes Mellitus (T2DM) patients from two cohorts: EVAS (289 patients from Singapore) and NHANES (517) from the USA. Personalized systems biology models (digital twins) were constructed. We deduced disease dynamics from the individually parameterized metabolic network and predicted the evolution path of the metabolic health state. For each patient, we obtained an individual description of disease dynamics and predict an evolution path of the metabolic health state. Our predictive models achieve an ROC-AUC in the range 0.79-0.95 (sensitivity 80-92%, specificity 62-94%) in identifying phenotypes at the baseline and predicting future development of diabetic retinopathy and cataract progression among T2DM patients within 3 years from the baseline. The GMFA method is a step towards realizing the ultimate goal to develop practical predictive computational models for diagnostics based on systems biology. This tool has potential use in chronic disease management in medical practice. Supplementary Information The online version contains supplementary material available at 10.1007/s13755-023-00218-x.
Collapse
Affiliation(s)
- Arsen Batagov
- Mesh Bio Pte. Ltd., 10 Anson Rd, #22-02, 079903 Singapore, Singapore
| | - Rinkoo Dalan
- Department of Endocrinology, Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Andrew Wu
- Mesh Bio Pte. Ltd., 10 Anson Rd, #22-02, 079903 Singapore, Singapore
| | - Wenbin Lai
- Mesh Bio Pte. Ltd., 10 Anson Rd, #22-02, 079903 Singapore, Singapore
| | - Colin S. Tan
- Fundus Image Reading Center, National Healthcare Group Eye Institute, Singapore, Singapore
- Tan Tock Seng Hospital, National Healthcare Group Eye Institute, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- School of Biological Science (SBS), Nanyang Technological University, Singapore, Singapore
| |
Collapse
|
5
|
Cserző M, Eisenhaber B, Eisenhaber F, Magyar C, Simon I. The First Quarter Century of the Dense Alignment Surface Transmembrane Prediction Method. Int J Mol Sci 2023; 24:14016. [PMID: 37762320 PMCID: PMC10531424 DOI: 10.3390/ijms241814016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/05/2023] [Accepted: 09/09/2023] [Indexed: 09/29/2023] Open
Abstract
The dense alignment surface (DAS) transmembrane (TM) prediction method was first published more than 25 years ago. DAS was the one of the earliest tools to discriminate TM proteins from globular ones and to predict the sequence positions of TM helices in proteins with high accuracy from their amino acid sequence alone. The algorithmic improvements that followed in 2002 (DAS-TMfilter) made it one of the best performing tools among those relying on local sequence information for TM prediction. Since then, many more experimental data about membrane proteins (including thousands of 3D structures of membrane proteins) have accumulated but there has been no significant improvement concerning performance in the area of TM helix prediction tools. Here, we report a new implementation of the DAS-TMfilter prediction web server. We reevaluated the performance of the method using a five-times-larger, updated test dataset. We found that the method performs at essentially the same accuracy as the original even without any change to the parametrization of the program despite the much larger dataset. Thus, the approach captures the physico-chemistry of TM helices well, essentially solving this scientific problem.
Collapse
Affiliation(s)
- Miklós Cserző
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary; (M.C.); (C.M.)
- Department of Physiology, Faculty of Medicine, Semmelweis University, 1094 Budapest, Hungary
| | - Birgit Eisenhaber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore; (B.E.); (F.E.)
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore
- LASA—Lausitz Advanced Scientific Applications gGmbH, 02943 Weißwasser, Germany
| | - Frank Eisenhaber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore; (B.E.); (F.E.)
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore
- LASA—Lausitz Advanced Scientific Applications gGmbH, 02943 Weißwasser, Germany
- School of Biological Sciences, Nanyang Technological University (NTU), Singapore 637551, Singapore
| | - Csaba Magyar
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary; (M.C.); (C.M.)
| | - István Simon
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary; (M.C.); (C.M.)
| |
Collapse
|
6
|
Tantoso E, Eisenhaber B, Sinha S, Jensen LJ, Eisenhaber F. Did the early full genome sequencing of yeast boost gene function discovery? Biol Direct 2023; 18:46. [PMID: 37574542 PMCID: PMC10424406 DOI: 10.1186/s13062-023-00403-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 08/01/2023] [Indexed: 08/15/2023] Open
Abstract
BACKGROUND Although the genome of Saccharomyces cerevisiae (S. cerevisiae) was the first one of a eukaryote organism that was fully sequenced (in 1996), a complete understanding of the potential of encoded biomolecular mechanisms has not yet been achieved. Here, we wish to quantify how far the goal of a full list of S. cerevisiae gene functions still is. RESULTS The scientific literature about S. cerevisiae protein-coding genes has been mapped onto the yeast genome via the mentioning of names for genomic regions in scientific publications. The match was quantified with the ratio of a given gene name's occurrences to those of any gene names in the article. We find that ~ 230 elite genes with ≥ 75 full publication equivalents (FPEs, FPE = 1 is an idealized publication referring to just a single gene) command ~ 45% of all literature. At the same time, about two thirds of the genes (each with less than 10 FPEs) are described in just 12% of the literature (in average each such gene has just ~ 1.5% of the literature of an elite gene). About 600 genes have not been mentioned in any dedicated article. Compared with other groups of genes, the literature growth rates were highest for uncharacterized or understudied genes until late nineties of the twentieth century. Yet, these growth rates deteriorated and became negative thereafter. Thus, yeast function discovery for previously uncharacterized genes has returned to the level of ~ 1980. At the same time, literature for anyhow well-studied genes (with a threshold T10 (≥ 10 FPEs) and higher) remains steadily growing. CONCLUSIONS Did the early full genome sequencing of yeast boost gene function discovery? The data proves that the moment of publishing the full genome in reality coincides with the onset of decline of gene function discovery for previously uncharacterized genes. If the current status of literature about yeast molecular mechanisms can be extrapolated into the future, it will take about another ~ 50 years to complete the yeast gene function list. We found that a small group of scientific journals contributed extraordinarily to publishing early reports relevant to yeast gene function discoveries.
Collapse
Affiliation(s)
- Erwin Tantoso
- Agency for Science, Technology and Research (A*STAR), Bioinformatics Institute (BII), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore.
- Agency for Science, Technology and Research (A*STAR), Genome Institute of Singapore (GIS), 60 Biopolis Street, Singapore, 138672, Republic of Singapore.
| | - Birgit Eisenhaber
- Agency for Science, Technology and Research (A*STAR), Bioinformatics Institute (BII), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore.
- Agency for Science, Technology and Research (A*STAR), Genome Institute of Singapore (GIS), 60 Biopolis Street, Singapore, 138672, Republic of Singapore.
- LASA - Lausitz Advanced Scientific Applications gGmbH, Straße Der Einheit 2-24, 02943, Weißwasser, Federal Republic of Germany.
| | - Swati Sinha
- European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Lars Juhl Jensen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Frank Eisenhaber
- Agency for Science, Technology and Research (A*STAR), Bioinformatics Institute (BII), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore.
- Agency for Science, Technology and Research (A*STAR), Genome Institute of Singapore (GIS), 60 Biopolis Street, Singapore, 138672, Republic of Singapore.
- LASA - Lausitz Advanced Scientific Applications gGmbH, Straße Der Einheit 2-24, 02943, Weißwasser, Federal Republic of Germany.
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Republic of Singapore.
| |
Collapse
|
7
|
Tromp J, van der Meer P, Tay WT, Ling LH, Loh SY, Soon D, Chin C, Jaufeerally F, Bamadhaj S, Ng TP, Lee SSG, Sim D, Yeo PSD, Leong GKT, Ong HY, Tantoso E, Eisenhaber F, Richards AM, Lam CSP. Diagnostic Accuracy of the Electrocardiogram for Heart Failure With Reduced or Preserved Ejection Fraction. J Card Fail 2023; 29:1104-1106. [PMID: 37004866 DOI: 10.1016/j.cardfail.2023.03.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 04/04/2023]
Affiliation(s)
- Jasper Tromp
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore; National Heart Centre Singapore, Singapore; University Medical Center Groningen, Groningen, the Netherlands; Duke-NUS Medical School, Singapore, Singapore
| | | | | | - Lieng Hsi Ling
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | | | | | | | | | - Tze Pin Ng
- University Medical Center Groningen, Groningen, the Netherlands
| | | | - David Sim
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore; University Medical Center Groningen, Groningen, the Netherlands
| | | | | | | | - Erwin Tantoso
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore
| | | | - Carolyn S P Lam
- National Heart Centre Singapore, Singapore; University Medical Center Groningen, Groningen, the Netherlands
| |
Collapse
|
8
|
Tantoso E, Eisenhaber B, Sinha S, Jensen LJ, Eisenhaber F. About the dark corners in the gene function space of Escherichia coli remaining without illumination by scientific literature. Biol Direct 2023; 18:7. [PMID: 36855185 PMCID: PMC9976479 DOI: 10.1186/s13062-023-00362-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 02/21/2023] [Indexed: 03/02/2023] Open
Abstract
BACKGROUND Although Escherichia coli (E. coli) is the most studied prokaryote organism in the history of life sciences, many molecular mechanisms and gene functions encoded in its genome remain to be discovered. This work aims at quantifying the illumination of the E. coli gene function space by the scientific literature and how close we are towards the goal of a complete list of E. coli gene functions. RESULTS The scientific literature about E. coli protein-coding genes has been mapped onto the genome via the mentioning of names for genomic regions in scientific articles both for the case of the strain K-12 MG1655 as well as for the 95%-threshold softcore genome of 1324 E. coli strains with known complete genome. The article match was quantified with the ratio of a given gene name's occurrence to the mentioning of any gene names in the paper. The various genome regions have an extremely uneven literature coverage. A group of elite genes with ≥ 100 full publication equivalents (FPEs, FPE = 1 is an idealized publication devoted to just a single gene) attracts the lion share of the papers. For K-12, ~ 65% of the literature covers just 342 elite genes; for the softcore genome, ~ 68% of the FPEs is about only 342 elite gene families (GFs). We also find that most genes/GFs have at least one mentioning in a dedicated scientific article (with the exception of at least 137 protein-coding transcripts for K-12 and 26 GFs from the softcore genome). Whereas the literature growth rates were highest for uncharacterized or understudied genes until 2005-2010 compared with other groups of genes, they became negative thereafter. At the same time, literature for anyhow well-studied genes started to grow explosively with threshold T10 (≥ 10 FPEs). Typically, a body of ~ 20 actual articles generated over ~ 15 years of research effort was necessary to reach T10. Lineage-specific co-occurrence analysis of genes belonging to the accessory genome of E. coli together with genomic co-localization and sequence-analytic exploration hints previously completely uncharacterized genes yahV and yddL being associated with osmotic stress response/motility mechanisms. CONCLUSION If the numbers of scientific articles about uncharacterized and understudied genes remain at least at present levels, full gene function lists for the strain K-12 MG1655 and the E. coli softcore genome are in reach within the next 25-30 years. Once the literature body for a gene crosses 10 FPEs, most of the critical fundamental research risk appears overcome and steady incremental research becomes possible.
Collapse
Affiliation(s)
- Erwin Tantoso
- Agency for Science, Technology and Research (A*STAR), Genome Institute of Singapore (GIS), 60 Biopolis Street, Singapore, 138672, Republic of Singapore.,Agency for Science, Technology and Research (A*STAR), Bioinformatics Institute (BII), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore
| | - Birgit Eisenhaber
- Agency for Science, Technology and Research (A*STAR), Genome Institute of Singapore (GIS), 60 Biopolis Street, Singapore, 138672, Republic of Singapore.,Agency for Science, Technology and Research (A*STAR), Bioinformatics Institute (BII), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore
| | - Swati Sinha
- Agency for Science, Technology and Research (A*STAR), Genome Institute of Singapore (GIS), 60 Biopolis Street, Singapore, 138672, Republic of Singapore.,Agency for Science, Technology and Research (A*STAR), Bioinformatics Institute (BII), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Lars Juhl Jensen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Frank Eisenhaber
- Agency for Science, Technology and Research (A*STAR), Genome Institute of Singapore (GIS), 60 Biopolis Street, Singapore, 138672, Republic of Singapore. .,Agency for Science, Technology and Research (A*STAR), Bioinformatics Institute (BII), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore. .,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Republic of Singapore.
| |
Collapse
|
9
|
Tantoso E, Eisenhaber B, Kirsch M, Shitov V, Zhao Z, Eisenhaber F. To kill or to be killed: pangenome analysis of Escherichia coli strains reveals a tailocin specific for pandemic ST131. BMC Biol 2022; 20:146. [PMID: 35710371 PMCID: PMC9205054 DOI: 10.1186/s12915-022-01347-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 06/08/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Escherichia coli (E. coli) has been one of the most studied model organisms in the history of life sciences. Initially thought just to be commensal bacteria, E. coli has shown wide phenotypic diversity including pathogenic isolates with great relevance to public health. Though pangenome analysis has been attempted several times, there is no systematic functional characterization of the E. coli subgroups according to the gene profile. RESULTS Systematically scanning for optimal parametrization, we have built the E. coli pangenome from 1324 complete genomes. The pangenome size is estimated to be ~25,000 gene families (GFs). Whereas the core genome diminishes as more genomes are added, the softcore genome (≥95% of strains) is stable with ~3000 GFs regardless of the total number of genomes. Apparently, the softcore genome (with a 92% or 95% generation threshold) can define the genome of a bacterial species listing the critically relevant, evolutionarily most conserved or important classes of GFs. Unsupervised clustering of common E. coli sequence types using the presence/absence GF matrix reveals distinct characteristics of E. coli phylogroups B1, B2, and E. We highlight the bi-lineage nature of B1, the variation of the secretion and of the iron acquisition systems in ST11 (E), and the incorporation of a highly conserved prophage into the genome of ST131 (B2). The tail structure of the prophage is evolutionarily related to R2-pyocin (a tailocin) from Pseudomonas aeruginosa PAO1. We hypothesize that this molecular machinery is highly likely to play an important role in protecting its own colonies; thus, contributing towards the rapid rise of pandemic E. coli ST131. CONCLUSIONS This study has explored the optimized pangenome development in E. coli. We provide complete GF lists and the pangenome matrix as supplementary data for further studies. We identified biological characteristics of different E. coli subtypes, specifically for phylogroups B1, B2, and E. We found an operon-like genome region coding for a tailocin specific for ST131 strains. The latter is a potential killer weapon providing pandemic E. coli ST131 with an advantage in inter-bacterial competition and, suggestively, explains their dominance as human pathogen among E. coli strains.
Collapse
Affiliation(s)
- Erwin Tantoso
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Republic of Singapore.,Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore
| | - Birgit Eisenhaber
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Republic of Singapore.,Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore
| | - Miles Kirsch
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore.,Present address: Northeastern University, Boston, USA
| | - Vladimir Shitov
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore
| | - Zhiya Zhao
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore.,Present address: The University of Cambridge, Cambridge, UK
| | - Frank Eisenhaber
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Republic of Singapore. .,Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore. .,School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, 637551, Singapore, Republic of Singapore.
| |
Collapse
|
10
|
Alfatah M, Eisenhaber F. The PICLS high-throughput screening method for agents extending cellular longevity identifies 2,5-anhydro-D-mannitol as novel anti-aging compound. GeroScience 2022; 45:141-158. [PMID: 35705837 PMCID: PMC9886722 DOI: 10.1007/s11357-022-00598-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/25/2022] [Indexed: 02/03/2023] Open
Abstract
Although aging is the biggest risk factor for human chronic (cancer, diabetic, cardiovascular, and neurodegenerative) diseases, few interventions are known besides caloric restriction and a small number of drugs (with substantial side effects) that directly address aging. Thus, there is an urgent need for new options that can generally delay aging processes and prevent age-related diseases. Cellular aging is at the basis of aging processes. Chronological lifespan (CLS) of yeast Saccharomyces cerevisiae is the well-established model system for investigating the interventions of human post-mitotic cellular aging. CLS is defined as the number of days cells remain viable in a stationary phase. We developed a new, cheap, and fast quantitative method for measuring CLS in cell cultures incubated together with various chemical agents and controls on 96-well plates. Our PICLS protocol with (1) the use of propidium iodide for fluorescent-based cell survival reading in a microplate reader and (2) total cell count measurement via OD600nm absorption from the same plate provides real high-throughput capacity. Depending on logistics, large numbers of plates can be processed in parallel so that the screening of thousands of compounds becomes feasible in a short time. The method was validated by measuring the effect of rapamycin and calorie restriction on yeast CLS. We utilized this approach for chemical agent screening. We discovered the anti-aging/geroprotective potential of 2,5-anhydro-D-mannitol (2,5-AM) and suggest its usage individually or in combination with other anti-aging interventions.
Collapse
Affiliation(s)
- Mohammad Alfatah
- Bioinformatics Institute (BII), Singapore, 138671, A*STAR, Singapore.
| | - Frank Eisenhaber
- Bioinformatics Institute (BII), Singapore, 138671, A*STAR, Singapore. .,Genome Institute of Singapore (GIS), Singapore, 138672, A*STAR, Singapore. .,School of Biological Sciences (SBS), Nanyang Technological University (NTU), Singapore, 637551, Singapore.
| |
Collapse
|
11
|
Tromp J, Seekings P, Hung CL, Iversen M, Frost M, Ouwerkerk W, Jiang Z, Eisenhaber F, Goh R, Huang W, Ling LH, Sim D, Cozzone P, Richards M, Lee HK, Solomon S, Lam SPC, Ezekowitz J. Automated Interpretation Of Systolic And Diastolic Function On The Echocardiogram. J Card Fail 2022. [DOI: 10.1016/j.cardfail.2022.03.266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
12
|
Jing JL, Ning TCY, Natali F, Eisenhaber F, Alfatah M. Iron Supplementation Delays Aging and Extends Cellular Lifespan through Potentiation of Mitochondrial Function. Cells 2022; 11:cells11050862. [PMID: 35269484 PMCID: PMC8909192 DOI: 10.3390/cells11050862] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/28/2022] [Accepted: 02/28/2022] [Indexed: 02/07/2023] Open
Abstract
Aging is the greatest challenge to humankind worldwide. Aging is associated with a progressive loss of physiological integrity due to a decline in cellular metabolism and functions. Such metabolic changes lead to age-related diseases, thereby compromising human health for the remaining life. Thus, there is an urgent need to identify geroprotectors that regulate metabolic functions to target the aging biological processes. Nutrients are the major regulator of metabolic activities to coordinate cell growth and development. Iron is an important nutrient involved in several biological functions, including metabolism. In this study using yeast as an aging model organism, we show that iron supplementation delays aging and increases the cellular lifespan. To determine how iron supplementation increases lifespan, we performed a gene expression analysis of mitochondria, the main cellular hub of iron utilization. Quantitative analysis of gene expression data reveals that iron supplementation upregulates the expression of the mitochondrial tricarboxylic acid (TCA) cycle and electron transport chain (ETC) genes. Furthermore, in agreement with the expression profiles of mitochondrial genes, ATP level is elevated by iron supplementation, which is required for increasing the cellular lifespan. To confirm, we tested the role of iron supplementation in the AMPK knockout mutant. AMPK is a highly conserved controller of mitochondrial metabolism and energy homeostasis. Remarkably, iron supplementation rescued the short lifespan of the AMPK knockout mutant and confirmed its anti-aging role through the enhancement of mitochondrial functions. Thus, our results suggest a potential therapeutic use of iron supplementation to delay aging and prolong healthspan.
Collapse
Affiliation(s)
- Jovian Lin Jing
- Bioinformatics Institute (BII), A*STAR, Singapore 138671, Singapore; (J.L.J.); (T.C.Y.N.)
| | - Trishia Cheng Yi Ning
- Bioinformatics Institute (BII), A*STAR, Singapore 138671, Singapore; (J.L.J.); (T.C.Y.N.)
| | - Federica Natali
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), A*STAR, Singapore 138669, Singapore;
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), Singapore 637551, Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute (BII), A*STAR, Singapore 138671, Singapore; (J.L.J.); (T.C.Y.N.)
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), Singapore 637551, Singapore
- Genome Institute of Singapore (GIS), A*STAR, Singapore 138672, Singapore
- Correspondence: (F.E.); (M.A.)
| | - Mohammad Alfatah
- Bioinformatics Institute (BII), A*STAR, Singapore 138671, Singapore; (J.L.J.); (T.C.Y.N.)
- Correspondence: (F.E.); (M.A.)
| |
Collapse
|
13
|
Eisenhaber F, Thakar J, Ponte-Sucre A, Dandekar T. Editorial: Innovative Strategies From Synthetic Biology and Bacterial Pathways to Master Biochemical Environmental Challenges. Front Bioeng Biotechnol 2022; 9:828632. [PMID: 35087812 PMCID: PMC8787148 DOI: 10.3389/fbioe.2021.828632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 12/13/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Frank Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University (NTU), Singapore, Singapore
| | - Juilee Thakar
- Department of Microbiology and Immunology, Department of Biomedical Genetics and Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY, United States
| | - Alicia Ponte-Sucre
- Laboratorio de Fisiología Molecular, Instituto de Medicina Experimental, Escuela Luis Razetti, Medical Mission Institute, Universidad Central de Venezuela, Würzburg, Germany
| | - Thomas Dandekar
- Department of Bioinformatics, Functional Genomics and Systems Biology Group, Biocenter, University of Würzburg, Würzburg, Germany
- *Correspondence: Thomas Dandekar,
| |
Collapse
|
14
|
Tantoso E, Eisenhaber B, Eisenhaber F. Optimizing the Parametrization of Homologue Classification in the Pan-Genome Computation for a Bacterial Species: Case Study Streptococcus pyogenes. Methods Mol Biol 2022; 2449:299-324. [PMID: 35507269 DOI: 10.1007/978-1-0716-2095-3_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The paradigm shift associated with the introduction of the pan-genome concept has drawn the attention from singular reference genomes toward the actual sequence diversity within organism populations, strain collections, clades, etc. A single genome is no longer sufficient to describe bacteria of interest, but instead, the genomic repertoire of all existing strains is the key to the metabolic, evolutionary, or pathogenic potential of a species. The classification of orthologous genes derived from a collection of taxonomically related genome sequences is central to bacterial pan-genome computational analysis. In this work, we present a review of methods for computing pan-genome gene clusters including their comparative analysis for the case of Streptococcus pyogenes strain genomes. We exhaustively scanned the parametrization space of the homologue searching procedures and find optimal parameters (sequence identity (60%) and coverage (50-60%) in the pairwise alignment) for the orthologous clustering of gene sequences. We find that the sequence identity threshold influences the number of gene families ~3 times stronger than the sequence coverage threshold.
Collapse
Affiliation(s)
- Erwin Tantoso
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Birgit Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
- Genome Institute Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Frank Eisenhaber
- Genome Institute and Bioinformatics Institute, Singapore, Singapore.
| |
Collapse
|
15
|
Szenker-Ravi E, Ott T, Khatoo M, Moreau de Bellaing A, Goh WX, Chong YL, Beckers A, Kannesan D, Louvel G, Anujan P, Ravi V, Bonnard C, Moutton S, Schoen P, Fradin M, Colin E, Megarbane A, Daou L, Chehab G, Di Filippo S, Rooryck C, Deleuze JF, Boland A, Arribard N, Eker R, Tohari S, Ng AYJ, Rio M, Lim CT, Eisenhaber B, Eisenhaber F, Venkatesh B, Amiel J, Crollius HR, Gordon CT, Gossler A, Roy S, Attie-Bitach T, Blum M, Bouvagnet P, Reversade B. Discovery of a genetic module essential for assigning left-right asymmetry in humans and ancestral vertebrates. Nat Genet 2022; 54:62-72. [PMID: 34903892 DOI: 10.1038/s41588-021-00970-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 10/14/2021] [Indexed: 01/24/2023]
Abstract
The vertebrate left-right axis is specified during embryogenesis by a transient organ: the left-right organizer (LRO). Species including fish, amphibians, rodents and humans deploy motile cilia in the LRO to break bilateral symmetry, while reptiles, birds, even-toed mammals and cetaceans are believed to have LROs without motile cilia. We searched for genes whose loss during vertebrate evolution follows this pattern and identified five genes encoding extracellular proteins, including a putative protease with hitherto unknown functions that we named ciliated left-right organizer metallopeptide (CIROP). Here, we show that CIROP is specifically expressed in ciliated LROs. In zebrafish and Xenopus, CIROP is required solely on the left side, downstream of the leftward flow, but upstream of DAND5, the first asymmetrically expressed gene. We further ascertained 21 human patients with loss-of-function CIROP mutations presenting with recessive situs anomalies. Our findings posit the existence of an ancestral genetic module that has twice disappeared during vertebrate evolution but remains essential for distinguishing left from right in humans.
Collapse
Affiliation(s)
- Emmanuelle Szenker-Ravi
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore (GIS), A*STAR, Singapore, Singapore.
| | - Tim Ott
- Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Muznah Khatoo
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore (GIS), A*STAR, Singapore, Singapore
| | - Anne Moreau de Bellaing
- Laboratoire de Cardiogénétique, Groupe Hospitalier Est, Hospices Civils de Lyon, Lyon, France
| | - Wei Xuan Goh
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore (GIS), A*STAR, Singapore, Singapore
| | - Yan Ling Chong
- Institute of Molecular and Cell Biology (IMCB), A*STAR, Singapore, Singapore
- Department of Pathology, National University Hospital, Singapore, Singapore
| | - Anja Beckers
- Institute for Molecular Biology, Hannover Medical School, Hannover, Germany
- REBIRTH Cluster of Excellence, Hannover, Germany
| | - Darshini Kannesan
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore (GIS), A*STAR, Singapore, Singapore
| | - Guillaume Louvel
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
- Écologie, Systématique et Évolution, UMR 8079 CNRS - Université Paris-Saclay - AgroParisTech, Orsay, France
| | - Priyanka Anujan
- Institute of Molecular and Cell Biology (IMCB), A*STAR, Singapore, Singapore
- Institute of Reproductive and Developmental Biology, Hammersmith Hospital, Imperial College, London, UK
| | - Vydianathan Ravi
- Institute of Molecular and Cell Biology (IMCB), A*STAR, Singapore, Singapore
| | - Carine Bonnard
- Skin Research Institute of Singapore (SRIS), A*STAR, Singapore, Singapore
| | - Sébastien Moutton
- CPDPN, Pôle mère enfant, Maison de Santé Protestante Bordeaux Bagatelle, Talence, France
| | | | - Mélanie Fradin
- Service de Génétique Médicale, Hôpital Sud, CHU de Rennes, Rennes, France
| | - Estelle Colin
- Service de Génétique Médicale, CHU d'Angers, Angers, France
| | - André Megarbane
- Department of Human Genetics, Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon
- Institut Jérôme LEJEUNE, Paris, France
| | - Linda Daou
- Department of Pediatric Cardiology, Hôtel Dieu de France University Medical Center, Saint Joseph University, Alfred Naccache Boulevard, Achrafieh, Beirut, Lebanon
| | - Ghassan Chehab
- Department of Pediatric Cardiology, Hôtel Dieu de France University Medical Center, Saint Joseph University, Alfred Naccache Boulevard, Achrafieh, Beirut, Lebanon
- Department of Pediatrics, Lebanese University, Faculty of Medical Sciences, Hadath, Greater Beirut, Lebanon
| | - Sylvie Di Filippo
- Service de Cardiologie Pédiatrique, Groupe Hospitalier Est, Hospices Civils de Lyon, Bron, France
| | - Caroline Rooryck
- Service de Génétique, University of Bordeaux, MRGM, INSERM U1211, CHU de Bordeaux, Bordeaux, France
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - Nicolas Arribard
- Service de Cardiologie Pédiatrique, Hôpital Universitaire des Enfants Reine Fabiola (HUDERF), Brussels, Belgium
| | - Rukiye Eker
- Pediatrics Department, Pediatric Cardiology Division, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
| | - Sumanty Tohari
- Institute of Molecular and Cell Biology (IMCB), A*STAR, Singapore, Singapore
| | - Alvin Yu-Jin Ng
- Molecular Diagnosis Centre (MDC), National University Hospital (NUH), Singapore, Singapore
| | - Marlène Rio
- Fédération de Génétique, Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, Paris, France
- Developmental Brain Disorders Laboratory, Université de Paris, Imagine Institute, INSERM UMR 1163, Paris, France
| | - Chun Teck Lim
- Bioinformatics Institute (BII), A*STAR, Singapore, Singapore
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), A*STAR, Singapore, Singapore
| | - Birgit Eisenhaber
- Bioinformatics Institute (BII), A*STAR, Singapore, Singapore
- Genome Institute of Singapore (GIS), A*STAR, Singapore, Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute (BII), A*STAR, Singapore, Singapore
- Genome Institute of Singapore (GIS), A*STAR, Singapore, Singapore
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), Singapore, Singapore
| | - Byrappa Venkatesh
- Institute of Molecular and Cell Biology (IMCB), A*STAR, Singapore, Singapore
- Department of Pediatrics, National University of Singapore (NUS), Singapore, Singapore
| | - Jeanne Amiel
- Fédération de Génétique, Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, Paris, France
- Laboratory of Embryology and Genetics of Malformations, Université de Paris, Imagine Institute, INSERM UMR 1163, Paris, France
| | - Hugues Roest Crollius
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
| | - Christopher T Gordon
- Laboratory of Embryology and Genetics of Malformations, Université de Paris, Imagine Institute, INSERM UMR 1163, Paris, France
| | - Achim Gossler
- Institute for Molecular Biology, Hannover Medical School, Hannover, Germany
- REBIRTH Cluster of Excellence, Hannover, Germany
| | - Sudipto Roy
- Institute of Molecular and Cell Biology (IMCB), A*STAR, Singapore, Singapore
- Department of Pediatrics, National University of Singapore (NUS), Singapore, Singapore
- Department of Biological Sciences, National University of Singapore (NUS), Singapore, Singapore
| | - Tania Attie-Bitach
- Fédération de Génétique, Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, Paris, France
- Laboratory of Genetics and Development of the Cerebral Cortex, Université de Paris, Imagine Institute, INSERM UMR 1163, Paris, France
| | - Martin Blum
- Institute of Biology, University of Hohenheim, Stuttgart, Germany.
| | | | - Bruno Reversade
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore (GIS), A*STAR, Singapore, Singapore.
- Institute of Molecular and Cell Biology (IMCB), A*STAR, Singapore, Singapore.
- Department of Pediatrics, National University of Singapore (NUS), Singapore, Singapore.
- Medical Genetics Department, Koç University School of Medicine (KUSOM), Istanbul, Turkey.
| |
Collapse
|
16
|
Tromp J, Seekings PJ, Hung CL, Iversen MB, Frost MJ, Ouwerkerk W, Jiang Z, Eisenhaber F, Goh RSM, Zhao H, Huang W, Ling LH, Sim D, Cozzone P, Richards AM, Lee HK, Solomon SD, Lam CSP, Ezekowitz JA. Automated interpretation of systolic and diastolic function on the echocardiogram: a multicohort study. Lancet Digit Health 2021; 4:e46-e54. [PMID: 34863649 DOI: 10.1016/s2589-7500(21)00235-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/24/2021] [Accepted: 10/07/2021] [Indexed: 12/21/2022]
Abstract
BACKGROUND Echocardiography is the diagnostic modality for assessing cardiac systolic and diastolic function to diagnose and manage heart failure. However, manual interpretation of echocardiograms can be time consuming and subject to human error. Therefore, we developed a fully automated deep learning workflow to classify, segment, and annotate two-dimensional (2D) videos and Doppler modalities in echocardiograms. METHODS We developed the workflow using a training dataset of 1145 echocardiograms and an internal test set of 406 echocardiograms from the prospective heart failure research platform (Asian Network for Translational Research and Cardiovascular Trials; ATTRaCT) in Asia, with previous manual tracings by expert sonographers. We validated the workflow against manual measurements in a curated dataset from Canada (Alberta Heart Failure Etiology and Analysis Research Team; HEART; n=1029 echocardiograms), a real-world dataset from Taiwan (n=31 241), the US-based EchoNet-Dynamic dataset (n=10 030), and in an independent prospective assessment of the Asian (ATTRaCT) and Canadian (Alberta HEART) datasets (n=142) with repeated independent measurements by two expert sonographers. FINDINGS In the ATTRaCT test set, the automated workflow classified 2D videos and Doppler modalities with accuracies (number of correct predictions divided by the total number of predictions) ranging from 0·91 to 0·99. Segmentations of the left ventricle and left atrium were accurate, with a mean Dice similarity coefficient greater than 93% for all. In the external datasets (n=1029 to 10 030 echocardiograms used as input), automated measurements showed good agreement with locally measured values, with a mean absolute error range of 9-25 mL for left ventricular volumes, 6-10% for left ventricular ejection fraction (LVEF), and 1·8-2·2 for the ratio of the mitral inflow E wave to the tissue Doppler e' wave (E/e' ratio); and reliably classified systolic dysfunction (LVEF <40%, area under the receiver operating characteristic curve [AUC] range 0·90-0·92) and diastolic dysfunction (E/e' ratio ≥13, AUC range 0·91-0·91), with narrow 95% CIs for AUC values. Independent prospective evaluation confirmed less variance of automated compared with human expert measurements, with all individual equivalence coefficients being less than 0 for all measurements. INTERPRETATION Deep learning algorithms can automatically annotate 2D videos and Doppler modalities with similar accuracy to manual measurements by expert sonographers. Use of an automated workflow might accelerate access, improve quality, and reduce costs in diagnosing and managing heart failure globally. FUNDING A*STAR Biomedical Research Council and A*STAR Exploit Technologies.
Collapse
Affiliation(s)
- Jasper Tromp
- National Heart Centre Singapore, Singapore; Duke-NUS Medical School, Singapore; Saw Swee Hock School of Public Health, National University of Singapore & National University Health System, Singapore
| | - Paul J Seekings
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore; Us2.ai, Singapore
| | - Chung-Lieh Hung
- Department of Medicine and Institute of Biomedical Sciences, Mackay Medical College, Taipei, Taiwan; Cardiovascular Division, Department of Internal Medicine, Mackay Memorial Hospital, Taipei, Taiwan
| | | | | | - Wouter Ouwerkerk
- National Heart Centre Singapore, Singapore; Department of Dermatology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection and Immunity Institute, Amsterdam, Netherlands
| | | | - Frank Eisenhaber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore; Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore; School of Biological Science, Nanyang Technological University, Singapore
| | - Rick S M Goh
- Institute of High Performance Computing, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Heng Zhao
- Institute of High Performance Computing, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Weimin Huang
- Institute for Infocomm Research, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Lieng-Hsi Ling
- National University Heart Centre, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - David Sim
- National Heart Centre Singapore, Singapore
| | - Patrick Cozzone
- Singapore Bioimaging Consortium, Biomedical Sciences Institutes, Agency for Science, Technology and Research (A*STAR), Singapore
| | - A Mark Richards
- National University Heart Centre, Singapore; Cardiovascular Research Institute, National University Health System, Singapore; Christchurch Heart Institute, University of Otago, Christchurch, New Zealand
| | - Hwee Kuan Lee
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore; Image and Pervasive Access Lab, CNRS UMI 2955, Singapore; Singapore Eye Research Institute, Singapore
| | - Scott D Solomon
- Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Carolyn S P Lam
- National Heart Centre Singapore, Singapore; Duke-NUS Medical School, Singapore; Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | | |
Collapse
|
17
|
Affiliation(s)
- Frank Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore.,Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore.,School of Biological Sciences, Nanyang Technological University (NTU), Singapore
| | - Chandra Verma
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore.,School of Biological Sciences, Nanyang Technological University (NTU), Singapore.,Department of Biological Sciences, National University of Singapore, Singapore
| | - Tom Blundell
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| |
Collapse
|
18
|
Sirota FL, Maurer-Stroh S, Li Z, Eisenhaber F, Eisenhaber B. Functional Classification of Super-Large Families of Enzymes Based on Substrate Binding Pocket Residues for Biocatalysis and Enzyme Engineering Applications. Front Bioeng Biotechnol 2021; 9:701120. [PMID: 34409021 PMCID: PMC8366029 DOI: 10.3389/fbioe.2021.701120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/12/2021] [Indexed: 11/13/2022] Open
Abstract
Large enzyme families such as the groups of zinc-dependent alcohol dehydrogenases (ADHs), long chain alcohol oxidases (AOxs) or amine dehydrogenases (AmDHs) with, sometimes, more than one million sequences in the non-redundant protein database and hundreds of experimentally characterized enzymes are excellent cases for protein engineering efforts aimed at refining and modifying substrate specificity. Yet, the backside of this wealth of information is that it becomes technically difficult to rationally select optimal sequence targets as well as sequence positions for mutagenesis studies. In all three cases, we approach the problem by starting with a group of experimentally well studied family members (including those with available 3D structures) and creating a structure-guided multiple sequence alignment and a modified phylogenetic tree (aka binding site tree) based just on a selection of potential substrate binding residue positions derived from experimental information (not from the full-length sequence alignment). Hereupon, the remaining, mostly uncharacterized enzyme sequences can be mapped; as a trend, sequence grouping in the tree branches follows substrate specificity. We show that this information can be used in the target selection for protein engineering work to narrow down to single suitable sequences and just a few relevant candidate positions for directed evolution towards activity for desired organic compound substrates. We also demonstrate how to find the closest thermophile example in the dataset if the engineering is aimed at achieving most robust enzymes.
Collapse
Affiliation(s)
- Fernanda L Sirota
- Bioinformatics Institute (BII), Agency for Science Technology and Research (ASTAR), Singapore, Singapore
| | - Sebastian Maurer-Stroh
- Bioinformatics Institute (BII), Agency for Science Technology and Research (ASTAR), Singapore, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Zhi Li
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute (BII), Agency for Science Technology and Research (ASTAR), Singapore, Singapore.,Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Birgit Eisenhaber
- Bioinformatics Institute (BII), Agency for Science Technology and Research (ASTAR), Singapore, Singapore.,Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| |
Collapse
|
19
|
Zhang Z, Yu J, Eisenhaber F, Gao X, Gojobori T. WITHDRAWN: In Memory of Vladimir B. Bajic (1952-2019). Genomics Proteomics Bioinformatics 2021:S1672-0229(21)00070-X. [PMID: 33744434 DOI: 10.1016/j.gpb.2019.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 12/05/2019] [Indexed: 11/21/2022]
Affiliation(s)
- Zhang Zhang
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Jun Yu
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Frank Eisenhaber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore
| | - Xin Gao
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Takashi Gojobori
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| |
Collapse
|
20
|
Eisenhaber B, Sinha S, Jadalanki CK, Shitov VA, Tan QW, Sirota FL, Eisenhaber F. Conserved sequence motifs in human TMTC1, TMTC2, TMTC3, and TMTC4, new O-mannosyltransferases from the GT-C/PMT clan, are rationalized as ligand binding sites. Biol Direct 2021; 16:4. [PMID: 33436046 PMCID: PMC7801869 DOI: 10.1186/s13062-021-00291-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 01/04/2021] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND The human proteins TMTC1, TMTC2, TMTC3 and TMTC4 have been experimentally shown to be components of a new O-mannosylation pathway. Their own mannosyl-transferase activity has been suspected but their actual enzymatic potential has not been demonstrated yet. So far, sequence analysis of TMTCs has been compromised by evolutionary sequence divergence within their membrane-embedded N-terminal region, sequence inaccuracies in the protein databases and the difficulty to interpret the large functional variety of known homologous proteins (mostly sugar transferases and some with known 3D structure). RESULTS Evolutionary conserved molecular function among TMTCs is only possible with conserved membrane topology within their membrane-embedded N-terminal regions leading to the placement of homologous long intermittent loops at the same membrane side. Using this criterion, we demonstrate that all TMTCs have 11 transmembrane regions. The sequence segment homologous to Pfam model DUF1736 is actually just a loop between TM7 and TM8 that is located in the ER lumen and that contains a small hydrophobic, but not membrane-embedded helix. Not only do the membrane-embedded N-terminal regions of TMTCs share a common fold and 3D structural similarity with subgroups of GT-C sugar transferases. The conservation of residues critical for catalysis, for binding of a divalent metal ion and of the phosphate group of a lipid-linked sugar moiety throughout enzymatically and structurally well-studied GT-Cs and sequences of TMTCs indicates that TMTCs are actually sugar-transferring enzymes. We present credible 3D structural models of all four TMTCs (derived from their closest known homologues 5ezm/5f15) and find observed conserved sequence motifs rationalized as binding sites for a metal ion and for a dolichyl-phosphate-mannose moiety. CONCLUSIONS With the results from both careful sequence analysis and structural modelling, we can conclusively say that the TMTCs are enzymatically active sugar transferases belonging to the GT-C/PMT superfamily. The DUF1736 segment, the loop between TM7 and TM8, is critical for catalysis and lipid-linked sugar moiety binding. Together with the available indirect experimental data, we conclude that the TMTCs are not only part of an O-mannosylation pathway in the endoplasmic reticulum of upper eukaryotes but, actually, they are the sought mannosyl-transferases.
Collapse
Affiliation(s)
- Birgit Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore.
- Genome Institute of Singapore (BII), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Republic of Singapore.
| | - Swati Sinha
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Chaitanya K Jadalanki
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Vladimir A Shitov
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
- Siberian State Medical University, Moskovskiy Trakt, 2, Tomsk, Tomsk Oblast, 634050, Russia
| | - Qiao Wen Tan
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
- School of Biological Science (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore, 637551, Republic of Singapore
| | - Fernanda L Sirota
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore.
- Genome Institute of Singapore (BII), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Republic of Singapore.
- School of Biological Science (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore, 637551, Republic of Singapore.
| |
Collapse
|
21
|
Su CTT, Sinha S, Eisenhaber B, Eisenhaber F. Structural modelling of the lumenal domain of human GPAA1, the metallo-peptide synthetase subunit of the transamidase complex, reveals zinc-binding mode and two flaps surrounding the active site. Biol Direct 2020; 15:14. [PMID: 32993792 PMCID: PMC7522609 DOI: 10.1186/s13062-020-00266-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 07/30/2020] [Indexed: 02/01/2023] Open
Abstract
Background The transamidase complex is a molecular machine in the endoplasmic reticulum of eukaryotes that attaches a glycosylphosphatidylinositol (GPI) lipid anchor to substrate proteins after cleaving a C-terminal propeptide with a defined sequence signal. Its five subunits are very hydrophobic; thus, solubility, heterologous expression and complex reconstruction are difficult. Therefore, theoretical approaches are currently the main source of insight into details of 3D structure and of the catalytic process. Results In this work, we generated model 3D structures of the lumenal domain of human GPAA1, the M28-type metallo-peptide-synthetase subunit of the transamidase, including zinc ion and model substrate positions. In comparative molecular dynamics (MD) simulations of M28-type structures and our GPAA1 models, we estimated the metal ion binding energies with evolutionary conserved amino acid residues in the catalytic cleft. We find that canonical zinc binding sites 2 and 3 are strongest binders for Zn1 and, where a second zinc is available, sites 2 and 4 for Zn2. Zinc interaction of site 5 with Zn1 enhances upon substrate binding in structures with only one zinc. Whereas a previously studied glutaminyl cyclase structure, the best known homologue to GPAA1, binds only one zinc ion at the catalytic site, GPAA1 can sterically accommodate two. The M28-type metallopeptidases segregate into two independent branches with regard to one/two zinc ion binding modality in a phylogenetic tree where the GPAA1 family is closer to the joint origin of both groups. For GPAA1 models, MD studies revealed two large loops (flaps) surrounding the active site being involved in an anti-correlated, breathing-like dynamics. Conclusions In the light of combined sequence-analytic and phylogenetic arguments as well as 3D structural modelling results, GPAA1 is most likely a single zinc ion metallopeptidase. Two large flaps environ the catalytic site restricting access to large substrates. Reviewers This article was reviewed by Thomas Dandekar (MD) and Michael Gromiha.
Collapse
Affiliation(s)
- Chinh Tran-To Su
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, # 07-01, Matrix, Singapore, 138671, Singapore
| | - Swati Sinha
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, # 07-01, Matrix, Singapore, 138671, Singapore
| | - Birgit Eisenhaber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, # 07-01, Matrix, Singapore, 138671, Singapore.
| | - Frank Eisenhaber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, # 07-01, Matrix, Singapore, 138671, Singapore. .,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
| |
Collapse
|
22
|
Maurer-Stroh S, Krutz NL, Kern PS, Gunalan V, Nguyen MN, Limviphuvadh V, Eisenhaber F, Gerberick GF. AllerCatPro-prediction of protein allergenicity potential from the protein sequence. Bioinformatics 2020; 35:3020-3027. [PMID: 30657872 PMCID: PMC6736023 DOI: 10.1093/bioinformatics/btz029] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 12/18/2018] [Accepted: 01/14/2019] [Indexed: 12/22/2022] Open
Abstract
Motivation Due to the risk of inducing an immediate Type I (IgE-mediated) allergic response, proteins intended for use in consumer products must be investigated for their allergenic potential before introduction into the marketplace. The FAO/WHO guidelines for computational assessment of allergenic potential of proteins based on short peptide hits and linear sequence window identity thresholds misclassify many proteins as allergens. Results We developed AllerCatPro which predicts the allergenic potential of proteins based on similarity of their 3D protein structure as well as their amino acid sequence compared with a data set of known protein allergens comprising of 4180 unique allergenic protein sequences derived from the union of the major databases Food Allergy Research and Resource Program, Comprehensive Protein Allergen Resource, WHO/International Union of Immunological Societies, UniProtKB and Allergome. We extended the hexamer hit rule by removing peptides with high probability of random occurrence measured by sequence entropy as well as requiring 3 or more hexamer hits consistent with natural linear epitope patterns in known allergens. This is complemented with a Gluten-like repeat pattern detection. We also switched from a linear sequence window similarity to a B-cell epitope-like 3D surface similarity window which became possible through extensive 3D structure modeling covering the majority (74%) of allergens. In case no structure similarity is found, the decision workflow reverts to the old linear sequence window rule. The overall accuracy of AllerCatPro is 84% compared with other current methods which range from 51 to 73%. Both the FAO/WHO rules and AllerCatPro achieve highest sensitivity but AllerCatPro provides a 37-fold increase in specificity. Availability and implementation https://allercatpro.bii.a-star.edu.sg/ Supplementary information Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Sebastian Maurer-Stroh
- Biomolecular Function Discovery Division, Bioinformatics Institute, Agency for Science, Technology and Research, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore
| | - Nora L Krutz
- The Procter & Gamble Services Company, Strombeek-Bever, Belgium
| | - Petra S Kern
- The Procter & Gamble Services Company, Strombeek-Bever, Belgium
| | - Vithiagaran Gunalan
- Biomolecular Function Discovery Division, Bioinformatics Institute, Agency for Science, Technology and Research, Singapore
| | - Minh N Nguyen
- Biomolecular Function Discovery Division, Bioinformatics Institute, Agency for Science, Technology and Research, Singapore
| | - Vachiranee Limviphuvadh
- Biomolecular Function Discovery Division, Bioinformatics Institute, Agency for Science, Technology and Research, Singapore
| | - Frank Eisenhaber
- Biomolecular Function Discovery Division, Bioinformatics Institute, Agency for Science, Technology and Research, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore
| | | |
Collapse
|
23
|
Goh F, Zhang MM, Lim TR, Low KN, Nge CE, Heng E, Yeo WL, Sirota FL, Crasta S, Tan Z, Ng V, Leong CY, Zhang H, Lezhava A, Chen SL, Hoon SS, Eisenhaber F, Eisenhaber B, Kanagasundaram Y, Wong FT, Ng SB. Identification and engineering of 32 membered antifungal macrolactone notonesomycins. Microb Cell Fact 2020; 19:71. [PMID: 32192516 PMCID: PMC7081687 DOI: 10.1186/s12934-020-01328-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 03/12/2020] [Indexed: 12/29/2022] Open
Abstract
Notonesomycin A is a 32-membered bioactive glycosylated macrolactone known to be produced by Streptomyces aminophilus subsp. notonesogenes 647-AV1 and S. aminophilus DSM 40186. In a high throughput antifungal screening campaign, we identified an alternative notonesomycin A producing strain, Streptomyces sp. A793, and its biosynthetic gene cluster. From this strain, we further characterized a new more potent antifungal non-sulfated analogue, named notonesomycin B. Through CRISPR–Cas9 engineering of the biosynthetic gene cluster, we were able to increase the production yield of notonesomycin B by up to 18-fold as well as generate a strain that exclusively produces this analogue.
Collapse
Affiliation(s)
- Falicia Goh
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Singapore.,Biotransformation Innovation Platform, A*STAR, 61 Biopolis Drive, Proteos Level 4, Singapore, 138673, Singapore
| | - Mingzi M Zhang
- Metabolic Engineering, Functional Molecules & Polymers, Institute of Chemical and Engineering Sciences, A*STAR, 31 Biopolis Way, Nanos #01-01, Singapore, 138669, Singapore.,Institute of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli County, Taiwan, R.O.C
| | - Tian Ru Lim
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Singapore
| | - Kia Ngee Low
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Singapore
| | - Choy Eng Nge
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Singapore
| | - Elena Heng
- Molecular Engineering Laboratory, Institute of Bioengineering and Nanotechnology, A*STAR, 31 Biopolis Way, Nanos, Singapore, 138669, Singapore
| | - Wan Lin Yeo
- Metabolic Engineering, Functional Molecules & Polymers, Institute of Chemical and Engineering Sciences, A*STAR, 31 Biopolis Way, Nanos #01-01, Singapore, 138669, Singapore
| | - Fernanda L Sirota
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Singapore
| | - Sharon Crasta
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Singapore
| | - Zann Tan
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Singapore
| | - Veronica Ng
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Singapore
| | - Chung Yan Leong
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Singapore
| | - Huibin Zhang
- Genome Institute of Singapore, A*STAR, 60 Biopolis Street, Genome #02-01, Singapore, 138672, Singapore
| | - Alexander Lezhava
- Genome Institute of Singapore, A*STAR, 60 Biopolis Street, Genome #02-01, Singapore, 138672, Singapore
| | - Swaine L Chen
- Genome Institute of Singapore, A*STAR, 60 Biopolis Street, Genome #02-01, Singapore, 138672, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, NUHS Tower Block, Level 10, Singapore, 119228, Singapore
| | - Shawn S Hoon
- Molecular Engineering Laboratory, Institute of Bioengineering and Nanotechnology, A*STAR, 31 Biopolis Way, Nanos, Singapore, 138669, Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Singapore.,School of Computer Science and Engineering, Nanyang Technological University (NTU), 50 Nanyang Drive, Singapore, 637553, Singapore
| | - Birgit Eisenhaber
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Singapore
| | | | - Fong T Wong
- Molecular Engineering Laboratory, Institute of Bioengineering and Nanotechnology, A*STAR, 31 Biopolis Way, Nanos, Singapore, 138669, Singapore.
| | - Siew Bee Ng
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Singapore.
| |
Collapse
|
24
|
Niska-Blakie J, Gopinathan L, Low KN, Kien YL, Goh CMF, Caldez MJ, Pfeiffenberger E, Jones OS, Ong CB, Kurochkin IV, Coppola V, Tessarollo L, Choi H, Kanagasundaram Y, Eisenhaber F, Maurer-Stroh S, Kaldis P. Knockout of the non-essential gene SUGCT creates diet-linked, age-related microbiome disbalance with a diabetes-like metabolic syndrome phenotype. Cell Mol Life Sci 2019; 77:3423-3439. [PMID: 31722069 PMCID: PMC7426296 DOI: 10.1007/s00018-019-03359-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 10/23/2019] [Accepted: 10/29/2019] [Indexed: 02/07/2023]
Abstract
SUGCT (C7orf10) is a mitochondrial enzyme that synthesizes glutaryl-CoA from glutarate in tryptophan and lysine catabolism, but it has not been studied in vivo. Although mutations in Sugct lead to Glutaric Aciduria Type 3 disease in humans, patients remain largely asymptomatic despite high levels of glutarate in the urine. To study the disease mechanism, we generated SugctKO mice and uncovered imbalanced lipid and acylcarnitine metabolism in kidney in addition to changes in the gut microbiome. After SugctKO mice were treated with antibiotics, metabolites were comparable to WT, indicating that the microbiome affects metabolism in SugctKO mice. SUGCT loss of function contributes to gut microbiota dysbiosis, leading to age-dependent pathological changes in kidney, liver, and adipose tissue. This is associated with an obesity-related phenotype that is accompanied by lipid accumulation in kidney and liver, as well as “crown-like” structures in adipocytes. Furthermore, we show that the SugctKO kidney pathology is accelerated and exacerbated by a high-lysine diet. Our study highlights the importance of non-essential genes with no readily detectable early phenotype, but with substantial contributions to the development of age-related pathologies, which result from an interplay between genetic background, microbiome, and diet in the health of mammals.
Collapse
Affiliation(s)
- Joanna Niska-Blakie
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), 61 Biopolis Drive, Proteos #3-09, Singapore, 138673, Republic of Singapore.,Bioinformatics Institute (BII), A*STAR, Singapore, 138671, Republic of Singapore
| | - Lakshmi Gopinathan
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), 61 Biopolis Drive, Proteos #3-09, Singapore, 138673, Republic of Singapore
| | - Kia Ngee Low
- Bioinformatics Institute (BII), A*STAR, Singapore, 138671, Republic of Singapore
| | - Yang Lay Kien
- Bioinformatics Institute (BII), A*STAR, Singapore, 138671, Republic of Singapore
| | - Christine M F Goh
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), 61 Biopolis Drive, Proteos #3-09, Singapore, 138673, Republic of Singapore
| | - Matias J Caldez
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), 61 Biopolis Drive, Proteos #3-09, Singapore, 138673, Republic of Singapore.,Department of Biochemistry, National University of Singapore (NUS), Singapore, 117597, Republic of Singapore
| | - Elisabeth Pfeiffenberger
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), 61 Biopolis Drive, Proteos #3-09, Singapore, 138673, Republic of Singapore
| | - Oliver S Jones
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), 61 Biopolis Drive, Proteos #3-09, Singapore, 138673, Republic of Singapore
| | - Chee Bing Ong
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), 61 Biopolis Drive, Proteos #3-09, Singapore, 138673, Republic of Singapore
| | - Igor V Kurochkin
- Bioinformatics Institute (BII), A*STAR, Singapore, 138671, Republic of Singapore
| | - Vincenzo Coppola
- Department of Cancer Biology and Genetics, The Ohio State University, 988 Biomedical Research Tower, 460 West 12th Ave, Columbus, OH, 43210, USA
| | - Lino Tessarollo
- Mouse Cancer Genetics Program, National Cancer Institute, NCI-Frederick, Bldg. 560, 1050 Boyles Street, Frederick, MD, 21702-1201, USA
| | - Hyungwon Choi
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), 61 Biopolis Drive, Proteos #3-09, Singapore, 138673, Republic of Singapore.,Department of Medicine, National University of Singapore (NUS), Singapore, 117597, Republic of Singapore
| | | | - Frank Eisenhaber
- Bioinformatics Institute (BII), A*STAR, Singapore, 138671, Republic of Singapore.,School of Computer Science and Engineering (SCSE), Nanyang Technological University (NTU), Singapore, 637553, Republic of Singapore
| | - Sebastian Maurer-Stroh
- Bioinformatics Institute (BII), A*STAR, Singapore, 138671, Republic of Singapore. .,Department of Biological Sciences (DBS), National University of Singapore (NUS), 14 Science Drive 4, Singapore, 117597, Republic of Singapore.
| | - Philipp Kaldis
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), 61 Biopolis Drive, Proteos #3-09, Singapore, 138673, Republic of Singapore. .,Department of Biochemistry, National University of Singapore (NUS), Singapore, 117597, Republic of Singapore. .,Department of Clinical Sciences, Lund University, Clinical Research Centre (CRC), Box 50332, 202 13, Malmö, Sweden.
| |
Collapse
|
25
|
Zhang Z, Yu J, Eisenhaber F, Gao X, Gojobori T. In Memory of Vladimir B. Bajic (1952–2019). Genomics, Proteomics & Bioinformatics 2019. [PMCID: PMC7056845 DOI: 10.1016/j.gpb.2019.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zhang Zhang
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- Corresponding author.
| | - Jun Yu
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Frank Eisenhaber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore
| | - Xin Gao
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Takashi Gojobori
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| |
Collapse
|
26
|
Eisenhaber B, Eisenhaber F. Darkness in the human gene and protein function space despite big omics data and decline in molecular mechanism discovery after 2000. Acta Crystallogr A Found Adv 2019. [DOI: 10.1107/s2053273319093756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
27
|
Toh YK, Shin J, Balakrishna AM, Kamariah N, Grüber A, Eisenhaber F, Eisenhaber B, Grüber G. Effect of the additional cysteine 503 of vancomycin-resistant Enterococcus faecalis (V583) alkylhydroperoxide reductase subunit F (AhpF) and the mechanism of AhpF and subunit C assembling. Free Radic Biol Med 2019; 138:10-22. [PMID: 31047989 DOI: 10.1016/j.freeradbiomed.2019.04.036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 04/17/2019] [Accepted: 04/26/2019] [Indexed: 01/31/2023]
Abstract
The vancomycin-resistant Enterococcus faecalis alkyl hydroperoxide reductase complex (AhpR) with its subunits AhpC (EfAhpC) and AhpF (EfAhpF) is of paramount importance to restore redox homeostasis. Therefore, knowledge about this defense system is essential to understand its antibiotic-resistance and survival in hosts. Recently, we described the crystallographic structures of EfAhpC, the two-fold thioredoxin-like domain of EfAhpF, the novel phenomenon of swapping of the catalytic domains of EfAhpF as well as the unique linker length, connecting the catalytically active N-and C-terminal domains of EfAhpF. Here, using mutagenesis and enzymatic studies, we reveal the effect of an additional third cysteine (C503) in EfAhpF, which might optimize the functional adaptation of the E. faecalis enzyme under various physiological conditions. The crystal structure and solution NMR data of the engineered C503A mutant of the thioredoxin-like domain of EfAhpF were used to describe alterations in the environment of the additional cysteine residue during modulation of the redox-state. To glean insight into the epitope and mechanism of EfAhpF and -AhpC interaction as well as the electron transfer from the thioredoxin-like domain of EfAhpF to AhpC, NMR-titration experiments were performed, showing a coordinated disappearance of peaks in the thioredoxin-like domain of EfAhpF in the presence of full length EfAhpC, and indicating a stable EfAhpF-AhpC-complex. Combined with docking studies, the interacting residues of EfAhpF were identified and a mechanism of electron transfer of the EfAhpF donor to the electron acceptor EfAhpC is described.
Collapse
Affiliation(s)
- Yew Kwang Toh
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Joon Shin
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore, 637551, Republic of Singapore
| | - Asha Manikkoth Balakrishna
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore, 637551, Republic of Singapore
| | - Neelagandan Kamariah
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore, 637551, Republic of Singapore
| | - Ardina Grüber
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore, 637551, Republic of Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore; School of Computer Science Engineering, Nanyang Technological University (NTU), 50 Nanyang Drive, Singapore, 637553, Republic of Singapore
| | - Birgit Eisenhaber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Gerhard Grüber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore; Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore, 637551, Republic of Singapore.
| |
Collapse
|
28
|
Tantoso E, Wong WC, Tay WH, Lee J, Sinha S, Eisenhaber B, Eisenhaber F. Hypocrisy Around Medical Patient Data: Issues of Access for Biomedical Research, Data Quality, Usefulness for the Purpose and Omics Data as Game Changer. Asian Bioeth Rev 2019; 11:189-207. [PMID: 33717311 PMCID: PMC7747340 DOI: 10.1007/s41649-019-00085-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 04/23/2019] [Accepted: 04/30/2019] [Indexed: 11/14/2022] Open
Abstract
Whether due to simplicity or hypocrisy, the question of access to patient data for biomedical research is widely seen in the public discourse only from the angle of patient privacy. At the same time, the desire to live and to live without disability is of much higher value to the patients. This goal can only be achieved by extracting research insight from patient data in addition to working on model organisms, something that is well understood by many patients. Yet, most biomedical researchers working outside of clinics and hospitals are denied access to patient records when, at the same time, clinicians who guard the patient data are not optimally prepared for the data’s analysis. Medical data collection is a time- and cost-intensive process that is most of all tedious, with few elements of intellectual and emotional satisfaction on its own. In this process, clinicians and bioinformaticians, each group with their own interests, have to join forces with the goal to generate medical data sets both from clinical trials and from routinely collected electronic health records that are, as much as possible, free from errors and obvious inconsistencies. The data cleansing effort as we have learned during curation of Singaporean clinical trial data is not a trivial task. The introduction of omics and sophisticated imaging modalities into clinical practice that are only partially interpreted in terms of diagnosis and therapy with today’s level of knowledge warrant the creation of clinical databases with full patient history. This opens up opportunities for re-analyses and cross-trial studies at future time points with more sophisticated analyses of the same data, the collection of which is very expensive.
Collapse
Affiliation(s)
- Erwin Tantoso
- Bioinformatics Institute (BII), Agency for Science and Technology (ASTAR), 30 Biopolis Street, #07-01, Matrix, Singapore, 138671 Singapore
| | - Wing-Cheong Wong
- Bioinformatics Institute (BII), Agency for Science and Technology (ASTAR), 30 Biopolis Street, #07-01, Matrix, Singapore, 138671 Singapore
| | - Wei Hong Tay
- Bioinformatics Institute (BII), Agency for Science and Technology (ASTAR), 30 Biopolis Street, #07-01, Matrix, Singapore, 138671 Singapore
| | - Joanne Lee
- Bioinformatics Institute (BII), Agency for Science and Technology (ASTAR), 30 Biopolis Street, #07-01, Matrix, Singapore, 138671 Singapore
| | - Swati Sinha
- Bioinformatics Institute (BII), Agency for Science and Technology (ASTAR), 30 Biopolis Street, #07-01, Matrix, Singapore, 138671 Singapore
| | - Birgit Eisenhaber
- Bioinformatics Institute (BII), Agency for Science and Technology (ASTAR), 30 Biopolis Street, #07-01, Matrix, Singapore, 138671 Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute (BII), Agency for Science and Technology (ASTAR), 30 Biopolis Street, #07-01, Matrix, Singapore, 138671 Singapore.,School of Computer Science and Engineering (SCSE), Nanyang Technological University (NTU), 50 Nanyang Drive, Singapore, 637553 Singapore
| |
Collapse
|
29
|
Sinha S, Nge CE, Leong CY, Ng V, Crasta S, Alfatah M, Goh F, Low KN, Zhang H, Arumugam P, Lezhava A, Chen SL, Kanagasundaram Y, Ng SB, Eisenhaber F, Eisenhaber B. Genomics-driven discovery of a biosynthetic gene cluster required for the synthesis of BII-Rafflesfungin from the fungus Phoma sp. F3723. BMC Genomics 2019; 20:374. [PMID: 31088369 PMCID: PMC6518819 DOI: 10.1186/s12864-019-5762-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 05/02/2019] [Indexed: 12/20/2022] Open
Abstract
Background Phomafungin is a recently reported broad spectrum antifungal compound but its biosynthetic pathway is unknown. We combed publicly available Phoma genomes but failed to find any putative biosynthetic gene cluster that could account for its biosynthesis. Results Therefore, we sequenced the genome of one of our Phoma strains (F3723) previously identified as having antifungal activity in a high-throughput screen. We found a biosynthetic gene cluster that was predicted to synthesize a cyclic lipodepsipeptide that differs in the amino acid composition compared to Phomafungin. Antifungal activity guided isolation yielded a new compound, BII-Rafflesfungin, the structure of which was determined. Conclusions We describe the NRPS-t1PKS cluster ‘BIIRfg’ compatible with the synthesis of the cyclic lipodepsipeptide BII-Rafflesfungin [HMHDA-L-Ala-L-Glu-L-Asn-L-Ser-L-Ser-D-Ser-D-allo-Thr-Gly]. We report new Stachelhaus codes for Ala, Glu, Asn, Ser, Thr, and Gly. We propose a mechanism for BII-Rafflesfungin biosynthesis, which involves the formation of the lipid part by BIIRfg_PKS followed by activation and transfer of the lipid chain by a predicted AMP-ligase on to the first PCP domain of the BIIRfg_NRPS gene. Electronic supplementary material The online version of this article (10.1186/s12864-019-5762-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Swati Sinha
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore.
| | - Choy-Eng Nge
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Chung Yan Leong
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Veronica Ng
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Sharon Crasta
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Mohammad Alfatah
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Falicia Goh
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Kia-Ngee Low
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Huibin Zhang
- Genome Institue of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, #02-01 Genome, Singapore, 138672, Republic of Singapore
| | - Prakash Arumugam
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Alexander Lezhava
- Genome Institue of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, #02-01 Genome, Singapore, 138672, Republic of Singapore
| | - Swaine L Chen
- Genome Institue of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, #02-01 Genome, Singapore, 138672, Republic of Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, NUHS Tower Block, Level 10, Singapore, 119228, Republic of Singapore
| | - Yoganathan Kanagasundaram
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Siew Bee Ng
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore.,School of Computer Science and Engineering (SCSE), Nanyang Technological University (NTU), 50 Nanyang Drive, Singapore, 637553, Republic of Singapore
| | - Birgit Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore.
| |
Collapse
|
30
|
Ng SB, Kanagasundaram Y, Fan H, Arumugam P, Eisenhaber B, Eisenhaber F. The 160K Natural Organism Library, a unique resource for natural products research. Nat Biotechnol 2018; 36:570-573. [PMID: 29979661 DOI: 10.1038/nbt.4187] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Siew Bee Ng
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Yoganathan Kanagasundaram
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Hao Fan
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Prakash Arumugam
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Birgit Eisenhaber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore.,School of Computer Engineering, Nanyang Technological University (NTU), Singapore, Republic of Singapore
| |
Collapse
|
31
|
Berger KA, Pigott DM, Tomlinson F, Godding D, Maurer-Stroh S, Taye B, Sirota FL, Han A, Lee RTC, Gunalan V, Eisenhaber F, Hay SI, Russell CA. The Geographic Variation of Surveillance and Zoonotic Spillover Potential of Influenza Viruses in Domestic Poultry and Swine. Open Forum Infect Dis 2018; 5:ofy318. [PMID: 30619908 PMCID: PMC6309522 DOI: 10.1093/ofid/ofy318] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 11/23/2018] [Indexed: 12/14/2022] Open
Abstract
Background Avian and swine influenza viruses circulate worldwide and pose threats to both animal and human health. The design of global surveillance strategies is hindered by information gaps on the geospatial variation in virus emergence potential and existing surveillance efforts. Methods We developed a spatial framework to quantify the geographic variation in outbreak emergence potential based on indices of potential for animal-to-human and secondary human-to-human transmission. We then compared our resultant raster model of variation in emergence potential with the global distribution of recent surveillance efforts from 359105 reports of surveillance activities. Results Our framework identified regions of Southeast Asia, Eastern Europe, Central America, and sub-Saharan Africa with high potential for influenza virus spillover. In the last 15 years, however, we found that 78.43% and 49.01% of high-risk areas lacked evidence of influenza virus surveillance in swine and domestic poultry, respectively. Conclusions Our work highlights priority areas where improved surveillance and outbreak mitigation could enhance pandemic preparedness strategies.
Collapse
Affiliation(s)
- Kathryn A Berger
- Department of Veterinary Medicine, University of Cambridge, United Kingdom.,Agrimetrics Ltd., Harpenden, United Kingdom
| | - David M Pigott
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
| | | | - David Godding
- Department of Veterinary Medicine, University of Cambridge, United Kingdom
| | | | - Biruhalem Taye
- Bioinformatics Institute, ASTAR, Singapore.,European Molecular Biology Laboratory, Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | | | - Alvin Han
- Bioinformatics Institute, ASTAR, Singapore.,National University of Singapore
| | | | | | - Frank Eisenhaber
- Bioinformatics Institute, ASTAR, Singapore.,National University of Singapore
| | - Simon I Hay
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
| | - Colin A Russell
- Academic Medical Center, University of Amsterdam, The Netherlands
| |
Collapse
|
32
|
Sinha S, Eisenhaber B, Jensen LJ, Kalbuaji B, Eisenhaber F. Darkness in the Human Gene and Protein Function Space: Widely Modest or Absent Illumination by the Life Science Literature and the Trend for Fewer Protein Function Discoveries Since 2000. Proteomics 2018; 18:e1800093. [PMID: 30265449 PMCID: PMC6282819 DOI: 10.1002/pmic.201800093] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/07/2018] [Indexed: 12/15/2022]
Abstract
The mentioning of gene names in the body of the scientific literature 1901-2017 and their fractional counting is used as a proxy to assess the level of biological function discovery. A literature score of one has been defined as full publication equivalent (FPE), the amount of literature necessary to achieve one publication solely dedicated to a gene. It has been found that less than 5000 human genes have each at least 100 FPEs in the available literature corpus. This group of elite genes (4817 protein-coding genes, 119 non-coding RNAs) attracts the overwhelming majority of the scientific literature about genes. Yet, thousands of proteins have never been mentioned at all, ≈2000 further proteins have not even one FPE of literature and, for ≈4600 additional proteins, the FPE count is below 10. The protein function discovery rate measured as numbers of proteins first mentioned or crossing a threshold of accumulated FPEs in a given year has grown until 2000 but is in decline thereafter. This drop is partially offset by function discoveries for non-coding RNAs. The full human genome sequencing does not boost the function discovery rate. Since 2000, the fastest growing group in the literature is that with at least 500 FPEs per gene.
Collapse
Affiliation(s)
- Swati Sinha
- Bioinformatics Institute (BII)Agency for Science and Technology (A*STAR)Matrix138671Singapore
| | - Birgit Eisenhaber
- Bioinformatics Institute (BII)Agency for Science and Technology (A*STAR)Matrix138671Singapore
| | - Lars Juhl Jensen
- Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenDK-2200 CopenhagenDenmark
| | - Bharata Kalbuaji
- Bioinformatics Institute (BII)Agency for Science and Technology (A*STAR)Matrix138671Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute (BII)Agency for Science and Technology (A*STAR)Matrix138671Singapore
- School of Computer Science and Engineering (SCSE)Nanyang Technological University (NTU)637553Singapore
| |
Collapse
|
33
|
Sirota FL, Goh F, Low KN, Yang LK, Crasta SC, Eisenhaber B, Eisenhaber F, Kanagasundaram Y, Ng SB. Isolation and Identification of an Anthracimycin Analogue from Nocardiopsis kunsanensis, a Halophile from a Saltern, by Genomic Mining Strategy. J Genomics 2018; 6:63-73. [PMID: 29805716 PMCID: PMC5970133 DOI: 10.7150/jgen.24368] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 04/25/2018] [Indexed: 11/23/2022] Open
Abstract
Modern medicine is unthinkable without antibiotics; yet, growing issues with microbial drug resistance require intensified search for new active compounds. Natural products generated by Actinobacteria have been a rich source of candidate antibiotics, for example anthracimycin that, so far, is only known to be produced by Streptomyces species. Based on sequence similarity with the respective biosynthetic cluster, we sifted through available microbial genome data with the goal to find alternative anthracimycin-producing organisms. In this work, we report about the prediction and experimental verification of the production of anthracimycin derivatives by Nocardiopsis kunsanensis, a non-Streptomyces actinobacterial microorganism. We discovered N. kunsanensis to predominantly produce a new anthracimycin derivative with methyl group at C-8 and none at C-2, labeled anthracimycin BII-2619, besides a minor amount of anthracimycin. It displays activity against Gram-positive bacteria with similar low level of mammalian cytotoxicity as that of anthracimycin.
Collapse
Affiliation(s)
- Fernanda L Sirota
- Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Republic of Singapore
| | - Falicia Goh
- Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Republic of Singapore
| | - Kia-Ngee Low
- Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Republic of Singapore
| | - Lay-Kien Yang
- Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Republic of Singapore
| | - Sharon C Crasta
- Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Republic of Singapore
| | - Birgit Eisenhaber
- Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Republic of Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Republic of Singapore.,School of Computer Engineering, Nanyang Technological University (NTU), 50 Nanyang Drive, Singapore 637553, Republic of Singapore
| | - Yoganathan Kanagasundaram
- Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Republic of Singapore
| | - Siew Bee Ng
- Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Republic of Singapore
| |
Collapse
|
34
|
Eisenhaber B, Sinha S, Wong WC, Eisenhaber F. Function of a membrane-embedded domain evolutionarily multiplied in the GPI lipid anchor pathway proteins PIG-B, PIG-M, PIG-U, PIG-W, PIG-V, and PIG-Z. Cell Cycle 2018; 17:874-880. [PMID: 29764287 PMCID: PMC6056205 DOI: 10.1080/15384101.2018.1456294] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Distant homology relationships among proteins with many transmembrane regions (TMs) are difficult to detect as they are clouded by the TMs’ hydrophobic compositional bias and mutational divergence in connecting loops. In the case of several GPI lipid anchor biosynthesis pathway components, the hidden evolutionary signal can be revealed with dissectHMMER, a sequence similarity search tool focusing on fold-critical, high complexity sequence segments. We find that a sequence module with 10 TMs in PIG-W, described as acyl transferase, is homologous to PIG-U, a transamidase subunit without characterized molecular function, and to mannosyltransferases PIG-B, PIG-M, PIG-V and PIG-Z. We conclude that this new, membrane-embedded domain named BindGPILA functions as the unit for recognizing, binding and stabilizing the GPI lipid anchor in a modification-competent form as this appears the only functional aspect shared among all proteins. Thus, PIG-U's likely molecular function is shuttling/presenting the anchor in a productive conformation to the transamidase complex.
Collapse
Affiliation(s)
- Birgit Eisenhaber
- a Bioinformatics Institute, Agency for Science , Technology and Research (A*STAR) , 30 Biopolis Street, #07-01 Matrix, Singapore 138671 , Republic of Singapore
| | - Swati Sinha
- a Bioinformatics Institute, Agency for Science , Technology and Research (A*STAR) , 30 Biopolis Street, #07-01 Matrix, Singapore 138671 , Republic of Singapore
| | - Wing-Cheong Wong
- a Bioinformatics Institute, Agency for Science , Technology and Research (A*STAR) , 30 Biopolis Street, #07-01 Matrix, Singapore 138671 , Republic of Singapore
| | - Frank Eisenhaber
- a Bioinformatics Institute, Agency for Science , Technology and Research (A*STAR) , 30 Biopolis Street, #07-01 Matrix, Singapore 138671 , Republic of Singapore.,b School of Computer Engineering , Nanyang Technological University (NTU) , 50 Nanyang Drive, Singapore 637553 , Republic of Singapore
| |
Collapse
|
35
|
Limviphuvadh V, Tan CS, Konishi F, Jenjaroenpun P, Xiang JS, Kremenska Y, Mu YS, Syn N, Lee SC, Soo RA, Eisenhaber F, Maurer-Stroh S, Yong WP. Discovering novel SNPs that are correlated with patient outcome in a Singaporean cancer patient cohort treated with gemcitabine-based chemotherapy. BMC Cancer 2018; 18:555. [PMID: 29751792 PMCID: PMC5948914 DOI: 10.1186/s12885-018-4471-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 05/01/2018] [Indexed: 12/20/2022] Open
Abstract
Background Single Nucleotide Polymorphisms (SNPs) can influence patient outcome such as drug response and toxicity after drug intervention. The purpose of this study is to develop a systematic pathway approach to accurately and efficiently predict novel non-synonymous SNPs (nsSNPs) that could be causative to gemcitabine-based chemotherapy treatment outcome in Singaporean non-small cell lung cancer (NSCLC) patients. Methods Using a pathway approach that incorporates comprehensive protein-protein interaction data to systematically extend the gemcitabine pharmacologic pathway, we identified 77 related nsSNPs, common in the Singaporean population. After that, we used five computational criteria to prioritize the SNPs based on their importance for protein function. We specifically selected and screened six candidate SNPs in a patient cohort with NSCLC treated with gemcitabine-based chemotherapy. Result We performed survival analysis followed by hematologic toxicity analyses and found that three of six candidate SNPs are significantly correlated with the patient outcome (P < 0.05) i.e. ABCG2 Q141K (rs2231142), SLC29A3 S158F (rs780668) and POLR2A N764K (rs2228130). Conclusions Our computational SNP candidate enrichment workflow approach was able to identify several high confidence biomarkers predictive for personalized drug treatment outcome while providing a rationale for a molecular mechanism of the SNP effect. Trial registration NCT00695994. Registered 10 June, 2008 ‘retrospectively registered’. Electronic supplementary material The online version of this article (10.1186/s12885-018-4471-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Vachiranee Limviphuvadh
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Singapore
| | - Chee Seng Tan
- Department of Haematology-Oncology, National University Health System, 5 Lower Kent Ridge Road, Singapore, 119074, Singapore
| | - Fumikazu Konishi
- Education Academy of Computational Life Sciences, Tokyo Institute of Technology, Tokyo, Japan
| | - Piroon Jenjaroenpun
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Singapore
| | - Joy Shengnan Xiang
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Singapore
| | - Yuliya Kremenska
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Singapore
| | - Yar Soe Mu
- Department of Haematology-Oncology, National University Health System, 5 Lower Kent Ridge Road, Singapore, 119074, Singapore
| | - Nicholas Syn
- Department of Haematology-Oncology, National University Health System, 5 Lower Kent Ridge Road, Singapore, 119074, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Soo Chin Lee
- Department of Haematology-Oncology, National University Health System, 5 Lower Kent Ridge Road, Singapore, 119074, Singapore
| | - Ross A Soo
- Department of Haematology-Oncology, National University Health System, 5 Lower Kent Ridge Road, Singapore, 119074, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Singapore.,Department of Biological Sciences, National University of Singapore (NUS), 14 Science Drive 4, Singapore, 117543, Singapore.,School of Computer Engineering (SCE), Nanyang Technological University (NTU), 50 Nanyang Drive, Singapore, 637553, Singapore
| | - Sebastian Maurer-Stroh
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Singapore.,Department of Biological Sciences, National University of Singapore (NUS), 14 Science Drive 4, Singapore, 117543, Singapore
| | - Wei Peng Yong
- Department of Haematology-Oncology, National University Health System, 5 Lower Kent Ridge Road, Singapore, 119074, Singapore.
| |
Collapse
|
36
|
Kamariah N, Eisenhaber B, Eisenhaber F, Grüber G. Active site C P-loop dynamics modulate substrate binding, catalysis, oligomerization, stability, over-oxidation and recycling of 2-Cys Peroxiredoxins. Free Radic Biol Med 2018; 118:59-70. [PMID: 29474868 DOI: 10.1016/j.freeradbiomed.2018.02.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 02/12/2018] [Accepted: 02/17/2018] [Indexed: 01/20/2023]
Abstract
Peroxiredoxins (Prxs) catalyse the rapid reduction of hydrogen peroxide, organic hydroperoxide and peroxynitrite, using a fully conserved peroxidatic cysteine (CP) located in a conserved sequence Pxxx(T/S)xxCP motif known as CP-loop. In addition, Prxs are involved in cellular signaling pathways and regulate several redox-dependent process related disease. The effective catalysis of Prxs is associated with alterations in the CP-loop between reduced, Fully Folded (FF), and oxidized, Locally Unfolded (LU) conformations, which are linked to dramatic changes in the oligomeric structure. Despite many studies, little is known about the precise structural and dynamic roles of the CP-loop on Prxs functions. Herein, the comprehensive biochemical and biophysical studies on Escherichia coli alkyl hydroperoxide reductase subunit C (EcAhpC) and the CP-loop mutants, EcAhpC-F45A and EcAhpC-F45P reveal that the reduced form of the CP-loop adopts conformational dynamics, which is essential for effective peroxide reduction. Furthermore, the point mutants alter the structure and dynamics of the reduced form of the CP-loop and, thereby, affect substrate binding, catalysis, oligomerization, stability and overoxidiation. In the oxidized form, due to restricted CP-loop dynamics, the EcAhpC-F45P mutant favours a decamer formation, which enhances the effective recycling by physiological reductases compared to wild-type EcAhpC. In addition, the study reveals that residue F45 increases the specificity of Prxs-reductase interactions. Based on these studies, we propose an evolution of the CP-loop with confined sequence conservation within Prxs subfamilies that might optimize the functional adaptation of Prxs into various physiological roles.
Collapse
Affiliation(s)
- Neelagandan Kamariah
- Bioinformatics Institute, Agency for Science, Technology and Research (A⁎STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Republic of Singapore
| | - Birgit Eisenhaber
- Bioinformatics Institute, Agency for Science, Technology and Research (A⁎STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Republic of Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute, Agency for Science, Technology and Research (A⁎STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Republic of Singapore; School of Computer Engineering, Nanyang Technological University (NTU), 50 Nanyang Drive, Singapore 637553, Republic of Singapore
| | - Gerhard Grüber
- Bioinformatics Institute, Agency for Science, Technology and Research (A⁎STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Republic of Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore.
| |
Collapse
|
37
|
Wong WC, Ng HK, Tantoso E, Soong R, Eisenhaber F. Finite-size effects in transcript sequencing count distribution: its power-law correction necessarily precedes downstream normalization and comparative analysis. Biol Direct 2018; 13:2. [PMID: 29433547 PMCID: PMC5809866 DOI: 10.1186/s13062-018-0204-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 01/23/2018] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Though earlier works on modelling transcript abundance from vertebrates to lower eukaroytes have specifically singled out the Zip's law, the observed distributions often deviate from a single power-law slope. In hindsight, while power-laws of critical phenomena are derived asymptotically under the conditions of infinite observations, real world observations are finite where the finite-size effects will set in to force a power-law distribution into an exponential decay and consequently, manifests as a curvature (i.e., varying exponent values) in a log-log plot. If transcript abundance is truly power-law distributed, the varying exponent signifies changing mathematical moments (e.g., mean, variance) and creates heteroskedasticity which compromises statistical rigor in analysis. The impact of this deviation from the asymptotic power-law on sequencing count data has never truly been examined and quantified. RESULTS The anecdotal description of transcript abundance being almost Zipf's law-like distributed can be conceptualized as the imperfect mathematical rendition of the Pareto power-law distribution when subjected to the finite-size effects in the real world; This is regardless of the advancement in sequencing technology since sampling is finite in practice. Our conceptualization agrees well with our empirical analysis of two modern day NGS (Next-generation sequencing) datasets: an in-house generated dilution miRNA study of two gastric cancer cell lines (NUGC3 and AGS) and a publicly available spike-in miRNA data; Firstly, the finite-size effects causes the deviations of sequencing count data from Zipf's law and issues of reproducibility in sequencing experiments. Secondly, it manifests as heteroskedasticity among experimental replicates to bring about statistical woes. Surprisingly, a straightforward power-law correction that restores the distribution distortion to a single exponent value can dramatically reduce data heteroskedasticity to invoke an instant increase in signal-to-noise ratio by 50% and the statistical/detection sensitivity by as high as 30% regardless of the downstream mapping and normalization methods. Most importantly, the power-law correction improves concordance in significant calls among different normalization methods of a data series averagely by 22%. When presented with a higher sequence depth (4 times difference), the improvement in concordance is asymmetrical (32% for the higher sequencing depth instance versus 13% for the lower instance) and demonstrates that the simple power-law correction can increase significant detection with higher sequencing depths. Finally, the correction dramatically enhances the statistical conclusions and eludes the metastasis potential of the NUGC3 cell line against AGS of our dilution analysis. CONCLUSIONS The finite-size effects due to undersampling generally plagues transcript count data with reproducibility issues but can be minimized through a simple power-law correction of the count distribution. This distribution correction has direct implication on the biological interpretation of the study and the rigor of the scientific findings. REVIEWERS This article was reviewed by Oliviero Carugo, Thomas Dandekar and Sandor Pongor.
Collapse
Affiliation(s)
- Wing-Cheong Wong
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore, 138671 Singapore
| | - Hong-kiat Ng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Erwin Tantoso
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore, 138671 Singapore
| | - Richie Soong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore, 138671 Singapore
- School of Computer Engineering (SCE), Nanyang Technological University (NTU), 50 Nanyang Drive, Singapore, 637553 Singapore
| |
Collapse
|
38
|
Toh YK, Balakrishna AM, Manimekalai MSS, Chionh BB, Seetharaman RRC, Eisenhaber F, Eisenhaber B, Grüber G. Novel insights into the vancomycin-resistant Enterococcus faecalis (V583) alkylhydroperoxide reductase subunit F. Biochim Biophys Acta Gen Subj 2017; 1861:3201-3214. [DOI: 10.1016/j.bbagen.2017.09.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 09/11/2017] [Accepted: 09/15/2017] [Indexed: 10/18/2022]
|
39
|
Marakasova ES, Eisenhaber B, Maurer-Stroh S, Eisenhaber F, Baranova A. Prenylation of viral proteins by enzymes of the host: Virus-driven rationale for therapy with statins and FT/GGT1 inhibitors. Bioessays 2017; 39. [DOI: 10.1002/bies.201700014] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
| | - Birgit Eisenhaber
- Bioinformatics Institute; Agency for Science; Technology and Research Singapore
| | - Sebastian Maurer-Stroh
- Bioinformatics Institute; Agency for Science; Technology and Research Singapore
- Department of Biological Sciences; National University Singapore; Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute; Agency for Science; Technology and Research Singapore
- Department of Biological Sciences; National University Singapore; Singapore
- School of Computer Engineering; Nanyang Technological University; Singapore
| | - Ancha Baranova
- School of Systems Biology; George Mason University; Fairfax VA USA
- Research Centre for Medical Genetics; Russian Academy of Medical Sciences; Moscow Russia
| |
Collapse
|
40
|
Amit M, Na'ara S, Francis D, Matanis W, Zolotov S, Eisenhaber B, Eisenhaber F, Weiler Sagie M, Malkin L, Billan S, Charas T, Gil Z. Post-translational Regulation of Radioactive Iodine Therapy Response in Papillary Thyroid Carcinoma. J Natl Cancer Inst 2017; 109:4108088. [DOI: 10.1093/jnci/djx092] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 04/20/2017] [Indexed: 02/06/2023] Open
|
41
|
Baker JA, Wong WC, Eisenhaber B, Warwicker J, Eisenhaber F. Charged residues next to transmembrane regions revisited: "Positive-inside rule" is complemented by the "negative inside depletion/outside enrichment rule". BMC Biol 2017; 15:66. [PMID: 28738801 PMCID: PMC5525207 DOI: 10.1186/s12915-017-0404-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 07/07/2017] [Indexed: 11/25/2022] Open
Abstract
Background Transmembrane helices (TMHs) frequently occur amongst protein architectures as means for proteins to attach to or embed into biological membranes. Physical constraints such as the membrane’s hydrophobicity and electrostatic potential apply uniform requirements to TMHs and their flanking regions; consequently, they are mirrored in their sequence patterns (in addition to TMHs being a span of generally hydrophobic residues) on top of variations enforced by the specific protein’s biological functions. Results With statistics derived from a large body of protein sequences, we demonstrate that, in addition to the positive charge preference at the cytoplasmic inside (positive-inside rule), negatively charged residues preferentially occur or are even enriched at the non-cytoplasmic flank or, at least, they are suppressed at the cytoplasmic flank (negative-not-inside/negative-outside (NNI/NO) rule). As negative residues are generally rare within or near TMHs, the statistical significance is sensitive with regard to details of TMH alignment and residue frequency normalisation and also to dataset size; therefore, this trend was obscured in previous work. We observe variations amongst taxa as well as for organelles along the secretory pathway. The effect is most pronounced for TMHs from single-pass transmembrane (bitopic) proteins compared to those with multiple TMHs (polytopic proteins) and especially for the class of simple TMHs that evolved for the sole role as membrane anchors. Conclusions The charged-residue flank bias is only one of the TMH sequence features with a role in the anchorage mechanisms, others apparently being the leucine intra-helix propensity skew towards the cytoplasmic side, tryptophan flanking as well as the cysteine and tyrosine inside preference. These observations will stimulate new prediction methods for TMHs and protein topology from a sequence as well as new engineering designs for artificial membrane proteins. Electronic supplementary material The online version of this article (doi:10.1186/s12915-017-0404-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- James Alexander Baker
- Bioinformatics Institute, Agency for Science Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix, Singapore, 138671, Singapore.,School of Chemistry, Manchester Institute of Biotechnology, 131 Princess Street, Manchester, M1 7DN, UK
| | - Wing-Cheong Wong
- Bioinformatics Institute, Agency for Science Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix, Singapore, 138671, Singapore
| | - Birgit Eisenhaber
- Bioinformatics Institute, Agency for Science Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix, Singapore, 138671, Singapore
| | - Jim Warwicker
- School of Chemistry, Manchester Institute of Biotechnology, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Frank Eisenhaber
- Bioinformatics Institute, Agency for Science Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix, Singapore, 138671, Singapore. .,School of Computer Engineering (SCE), Nanyang Technological University (NTU), 50 Nanyang Drive, Singapore, 637553, Singapore.
| |
Collapse
|
42
|
Taye B, Vaz C, Tanavde V, Kuznetsov VA, Eisenhaber F, Sugrue RJ, Maurer-Stroh S. Benchmarking selected computational gene network growing tools in context of virus-host interactions. Sci Rep 2017; 7:5805. [PMID: 28724991 PMCID: PMC5517527 DOI: 10.1038/s41598-017-06020-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 06/07/2017] [Indexed: 01/04/2023] Open
Abstract
Several available online tools provide network growing functions where an algorithm utilizing different data sources suggests additional genes/proteins that should connect an input gene set into functionally meaningful networks. Using the well-studied system of influenza host interactions, we compare the network growing function of two free tools GeneMANIA and STRING and the commercial IPA for their performance of recovering known influenza A virus host factors previously identified from siRNA screens. The result showed that given small (~30 genes) or medium (~150 genes) input sets all three network growing tools detect significantly more known host factors than random human genes with STRING overall performing strongest. Extending the networks with all the three tools significantly improved the detection of GO biological processes of known host factors compared to not growing networks. Interestingly, the rate of identification of true host factors using computational network growing is equal or better to doing another experimental siRNA screening study which could also be true and applied to other biological pathways/processes.
Collapse
Affiliation(s)
- Biruhalem Taye
- Bioinformatics Institute, A*STAR, 30 Biopolis Street #07-01 Matrix, Singapore, 138671, Singapore. .,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore. .,Aklilu Lemma Institute of Pathobiology, Addis Ababa University, P.O.BOX 1176, Addis Ababa, Ethiopia.
| | - Candida Vaz
- Bioinformatics Institute, A*STAR, 30 Biopolis Street #07-01 Matrix, Singapore, 138671, Singapore
| | - Vivek Tanavde
- Bioinformatics Institute, A*STAR, 30 Biopolis Street #07-01 Matrix, Singapore, 138671, Singapore.,Institute of Medical Biology, A*STAR, 8A Biomedical Grove, #06-06 Immunos, Singapore, 138648, Singapore
| | - Vladimir A Kuznetsov
- Bioinformatics Institute, A*STAR, 30 Biopolis Street #07-01 Matrix, Singapore, 138671, Singapore.,School of Computer Engineering, Nanyang Technological University, 50 Nanyang Drive, Singapore, 637553, Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute, A*STAR, 30 Biopolis Street #07-01 Matrix, Singapore, 138671, Singapore.,Department of Biological Sciences, National University of Singapore, 8 Medical Drive, Singapore, 117597, Singapore.,School of Computer Engineering, Nanyang Technological University, 50 Nanyang Drive, Singapore, 637553, Singapore
| | - Richard J Sugrue
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Sebastian Maurer-Stroh
- Bioinformatics Institute, A*STAR, 30 Biopolis Street #07-01 Matrix, Singapore, 138671, Singapore.,Department of Biological Sciences, National University of Singapore, 8 Medical Drive, Singapore, 117597, Singapore.,National Public Health Laboratory, Ministry of Health, 3 Biopolis Drive, Synapse #05-14/16, Singapore, 138623, Singapore
| |
Collapse
|
43
|
Kamariah N, Eisenhaber B, Eisenhaber F, Grüber G. Essential role of the flexible linker on the conformational equilibrium of bacterial peroxiredoxin reductase for effective regeneration of peroxiredoxin. J Biol Chem 2017; 292:6667-6679. [PMID: 28270505 DOI: 10.1074/jbc.m117.775858] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Revised: 02/27/2017] [Indexed: 12/13/2022] Open
Abstract
Reactive oxygen species (ROS) can damage DNA, proteins, and lipids, so cells have antioxidant systems that regulate ROS. In many bacteria, a dedicated peroxiredoxin reductase, alkyl hydroperoxide reductase subunit F (AhpF), catalyzes the rapid reduction of the redox-active disulfide center of the antioxidant protein peroxiredoxin (AhpC) to detoxify ROS such as hydrogen peroxide, organic hydroperoxide, and peroxynitrite. AhpF is a flexible multidomain protein that enables a series of electron transfers among the redox centers by accepting reducing equivalents from NADH. A flexible linker connecting the N-terminal domain (NTD) and C-terminal domain (CTD) of AhpF suggests that the enzyme adopts a large-scale domain motion that alternates between the closed and open states to shuttle electrons from the CTD via the NTD to AhpC. Here, we conducted comprehensive mutational, biochemical, and biophysical analyses to gain insights into the role of the flexible linker and the residues critical for the domain motions of Escherichia coli AhpF (EcAhpF) during electron transfer. Small-angle X-ray scattering studies of linker mutants revealed that a group of charged residues, 200EKR202, is crucial for the swiveling motion of the NTD. Moreover, NADH binding significantly affected EcAhpF flexibility and the movement of the NTD relative to the CTD. The mutants also exhibited a decrease in H2O2 reduction by the AhpF-AhpC ensemble. We propose that a concerted movement involving the NTD, C-terminal NADH, and FAD domains, and the flexible linker between them is essential for optimal intra-domain cross-talk and for efficient electron transfer to the redox partner AhpC required for peroxidation.
Collapse
Affiliation(s)
- Neelagandan Kamariah
- From the Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138671
| | - Birgit Eisenhaber
- From the Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138671
| | - Frank Eisenhaber
- From the Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138671.,the School of Computer Engineering, Nanyang Technological University, Singapore 637553, Republic of Singapore
| | - Gerhard Grüber
- From the Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138671, .,the School of Biological Sciences, Nanyang Technological University, Singapore 637551, and
| |
Collapse
|
44
|
Lua WH, Ling WL, Su CTT, Yeo JY, Verma CS, Eisenhaber B, Eisenhaber F, Gan SKE. Discovery of a novel splice variant of Fcar (CD89) unravels sequence segments necessary for efficient secretion: A story of bad signal peptides and good ones that nevertheless do not make it. Cell Cycle 2017; 16:457-467. [PMID: 28103138 PMCID: PMC5351921 DOI: 10.1080/15384101.2017.1281480] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
The IgA receptor, Fcar (CD89) consists of 5 sequence segments: 2 segments (S1, S2) forming the potential signal peptide, 2 extracellular EC domains that include the IgA binding site, and the transmembrane and cytoplasmic tail (TM/C) region. Numerous Fcar splice variants have been reported with various combinations of the sequence segments mentioned above. Here, we report a novel splice variant termed variant APD isolated from a healthy volunteer that lacks only the IgA-binding EC1 domain. Despite possessing the complete signal peptide S1+S2, the variant APD is only found in the intracellular space whereas the wild-type variant 1 is efficiently secreted and variant 4 leaks to the extracellular space. Further mutational experiments involving signal peptide replacements, cleavage site modifications, and studies on alternative isoforms demonstrate that despite the completeness of the signal peptide motif, the presence of the EC1 domain is essential for efficient extracellular export.
Collapse
Affiliation(s)
- Wai-Heng Lua
- a Bioinformatics Institute, Agency for Science, Technology, and Research (A*STAR) , Singapore
| | - Wei-Li Ling
- a Bioinformatics Institute, Agency for Science, Technology, and Research (A*STAR) , Singapore
| | - Chinh Tran-To Su
- a Bioinformatics Institute, Agency for Science, Technology, and Research (A*STAR) , Singapore
| | - Joshua Yi Yeo
- a Bioinformatics Institute, Agency for Science, Technology, and Research (A*STAR) , Singapore
| | - Chandra Shekhar Verma
- a Bioinformatics Institute, Agency for Science, Technology, and Research (A*STAR) , Singapore.,b Department of Biological Sciences , National University of Singapore (NUS) , Singapore.,c School of Biological Sciences, Nanyang Technological University (NTU) , Singapore
| | - Birgit Eisenhaber
- a Bioinformatics Institute, Agency for Science, Technology, and Research (A*STAR) , Singapore
| | - Frank Eisenhaber
- a Bioinformatics Institute, Agency for Science, Technology, and Research (A*STAR) , Singapore.,d School of Computer Engineering, Nanyang Technological University (NTU) , Singapore
| | - Samuel Ken-En Gan
- a Bioinformatics Institute, Agency for Science, Technology, and Research (A*STAR) , Singapore.,e p53 Laboratory, Agency for Science, Technology, and Research (A*STAR) , Singapore
| |
Collapse
|
45
|
Kurochkin IV, Guarnera E, Wong JH, Eisenhaber F, Berezovsky IN. Toward Allosterically Increased Catalytic Activity of Insulin-Degrading Enzyme against Amyloid Peptides. Biochemistry 2016; 56:228-239. [PMID: 27982586 DOI: 10.1021/acs.biochem.6b00783] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The physiological role of insulin-degrading enzyme (IDE) in the intracytosolic clearance of amyloid β (Aβ) and other amyloid-like peptides supports a hypothesis that human IDE hyperactivation could be therapeutically beneficial for the treatment of late-onset Alzheimer's disease (AD). The major challenge standing in the way of this goal is increasing the specific catalytic activity of IDE against the Aβ substrate. There were previous indications that the allosteric mode of IDE activity regulation could potentially provide a highly specific path toward degradation of amyloid-like peptides, while not dramatically affecting activity against other substrates. Recently developed theoretical concepts are used here to explore potential allosteric modulation of the IDE activity as a result of single-residue mutations. Five candidates are selected for experimental follow-up and allosteric free energy calculations: Ser137Ala, Lys396Ala, Asp426Ala, Phe807Ala, and Lys898Ala. Our experiments show that three mutations (Ser137Ala, Phe807Ala, and Lys898Ala) decrease the Km of the Aβ substrate. Mutation Lys898Ala results in increased catalytic activity of IDE; on the other hand, Lys364Ala does not change the activity and Asp426Ala diminishes it. Quantifying effects of mutations in terms of allosteric free energy, we show that favorable mutations lead to stabilization of the catalytic sites and other function-relevant distal sites as well as increased dynamics of the IDE-N and IDE-C halves that allow efficient substrate entrance and cleavage. A possibility for intramolecular upregulation of IDE activity against amyloid peptides via allosteric mutations calls for further investigations in this direction. Ultimately, we are hopeful it will lead to the development of IDE-based drugs for the treatment of the late-onset form of AD characterized by an overall impairment of Aβ clearance.
Collapse
Affiliation(s)
- Igor V Kurochkin
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR) , 30 Biopolis Street, #07-01, Matrix, Singapore 138671
| | - Enrico Guarnera
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR) , 30 Biopolis Street, #07-01, Matrix, Singapore 138671
| | - Jin H Wong
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR) , 30 Biopolis Street, #07-01, Matrix, Singapore 138671
| | - Frank Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR) , 30 Biopolis Street, #07-01, Matrix, Singapore 138671.,Department of Biological Sciences (DBS), National University of Singapore (NUS) , 8 Medical Drive, Singapore 117579.,School of Computer Engineering (SCE), Nanyang Technological University (NTU) , 50 Nanyang Drive, Singapore 637553
| | - Igor N Berezovsky
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR) , 30 Biopolis Street, #07-01, Matrix, Singapore 138671.,Department of Biological Sciences (DBS), National University of Singapore (NUS) , 8 Medical Drive, Singapore 117579
| |
Collapse
|
46
|
Yap CK, Eisenhaber B, Eisenhaber F, Wong WC. xHMMER3x2: Utilizing HMMER3's speed and HMMER2's sensitivity and specificity in the glocal alignment mode for improved large-scale protein domain annotation. Biol Direct 2016; 11:63. [PMID: 27894340 PMCID: PMC5126834 DOI: 10.1186/s13062-016-0163-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Accepted: 10/24/2016] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND While the local-mode HMMER3 is notable for its massive speed improvement, the slower glocal-mode HMMER2 is more exact for domain annotation by enforcing full domain-to-sequence alignments. Since a unit of domain necessarily implies a unit of function, local-mode HMMER3 alone remains insufficient for precise function annotation tasks. In addition, the incomparable E-values for the same domain model by different HMMER builds create difficulty when checking for domain annotation consistency on a large-scale basis. RESULTS In this work, both the speed of HMMER3 and glocal-mode alignment of HMMER2 are combined within the xHMMER3x2 framework for tackling the large-scale domain annotation task. Briefly, HMMER3 is utilized for initial domain detection so that HMMER2 can subsequently perform the glocal-mode, sequence-to-full-domain alignments for the detected HMMER3 hits. An E-value calibration procedure is required to ensure that the search space by HMMER2 is sufficiently replicated by HMMER3. We find that the latter is straightforwardly possible for ~80% of the models in the Pfam domain library (release 29). However in the case of the remaining ~20% of HMMER3 domain models, the respective HMMER2 counterparts are more sensitive. Thus, HMMER3 searches alone are insufficient to ensure sensitivity and a HMMER2-based search needs to be initiated. When tested on the set of UniProt human sequences, xHMMER3x2 can be configured to be between 7× and 201× faster than HMMER2, but with descending domain detection sensitivity from 99.8 to 95.7% with respect to HMMER2 alone; HMMER3's sensitivity was 95.7%. At extremes, xHMMER3x2 is either the slow glocal-mode HMMER2 or the fast HMMER3 with glocal-mode. Finally, the E-values to false-positive rates (FPR) mapping by xHMMER3x2 allows E-values of different model builds to be compared, so that any annotation discrepancies in a large-scale annotation exercise can be flagged for further examination by dissectHMMER. CONCLUSION The xHMMER3x2 workflow allows large-scale domain annotation speed to be drastically improved over HMMER2 without compromising for domain-detection with regard to sensitivity and sequence-to-domain alignment incompleteness. The xHMMER3x2 code and its webserver (for Pfam release 27, 28 and 29) are freely available at http://xhmmer3x2.bii.a-star.edu.sg/ . REVIEWERS Reviewed by Thomas Dandekar, L. Aravind, Oliviero Carugo and Shamil Sunyaev. For the full reviews, please go to the Reviewers' comments section.
Collapse
Affiliation(s)
- Choon-Kong Yap
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore, 138671, Singapore
| | - Birgit Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore, 138671, Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore, 138671, Singapore. .,School of Computer Engineering (SCE), Nanyang Technological University (NTU), 50 Nanyang Drive, Singapore, 637553, Singapore.
| | - Wing-Cheong Wong
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore, 138671, Singapore.
| |
Collapse
|
47
|
Kamariah N, Sek MF, Eisenhaber B, Eisenhaber F, Grüber G. Transition steps in peroxide reduction and a molecular switch for peroxide robustness of prokaryotic peroxiredoxins. Sci Rep 2016; 6:37610. [PMID: 27892488 PMCID: PMC5124861 DOI: 10.1038/srep37610] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 10/31/2016] [Indexed: 12/26/2022] Open
Abstract
In addition to their antioxidant function, the eukaryotic peroxiredoxins (Prxs) facilitate peroxide-mediated signaling by undergoing controlled inactivation by peroxide-driven over-oxidation. In general, the bacterial enzyme lacks this controlled inactivation mechanism, making it more resistant to high H2O2 concentrations. During peroxide reduction, the active site alternates between reduced, fully folded (FF), and oxidized, locally unfolded (LU) conformations. Here we present novel insights into the divergence of bacterial and human Prxs in robustness and sensitivity to inactivation, respectively. Structural details provide new insights into sub-steps during the catalysis of peroxide reduction, enabling the transition from an FF to a LU conformation. Complementary to mutational and enzymatic results, these data unravel the essential role of the C-terminal tail of bacterial Prxs to act as a molecular switch, mediating the transition from an FF to a LU state. In addition, we propose that the C-terminal tail has influence on the propensity of the disulphide bond formation, indicating that as a consequence on the robustness and sensitivity to over-oxidation. Finally, a physical linkage between the catalytic site, the C-terminal tail and the oligomer interface is described.
Collapse
Affiliation(s)
- Neelagandan Kamariah
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Republic of Singapore
| | - Mun Foong Sek
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Birgit Eisenhaber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Republic of Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Republic of Singapore.,School of Computer Engineering, Nanyang Technological University (NTU), 50 Nanyang Drive, Singapore 637553, Republic of Singapore
| | - Gerhard Grüber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Republic of Singapore.,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| |
Collapse
|
48
|
Berezovsky IN, Guarnera E, Zheng Z, Eisenhaber B, Eisenhaber F. Protein function machinery: from basic structural units to modulation of activity. Curr Opin Struct Biol 2016; 42:67-74. [PMID: 27865209 DOI: 10.1016/j.sbi.2016.10.021] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 09/26/2016] [Accepted: 10/31/2016] [Indexed: 11/29/2022]
Abstract
Contemporary protein structure is a result of the trade off between the laws of physics and the evolutionary selection. The polymer nature of proteins played a decisive role in establishing the basic structural and functional units of soluble proteins. We discuss how these elementary building blocks work in the hierarchy of protein domain structure, co-translational folding, as well as in enzymatic activity and molecular interactions. Next, we consider modulators of the protein function, such as intermolecular interactions, disorder-to-order transitions, and allosteric signaling, acting via interference with the protein's structural dynamics. We also discuss the post-translational modifications, which is a complementary intricate mechanism evolved for regulation of protein functions and interactions. In conclusion, we assess an anticipated contribution of discussed topics to the future advancements in the field.
Collapse
Affiliation(s)
- Igor N Berezovsky
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671, Singapore; Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive, Singapore 117579, Singapore.
| | - Enrico Guarnera
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671, Singapore
| | - Zejun Zheng
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671, Singapore
| | - Birgit Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671, Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671, Singapore; School of Computer Engineering (SCE), Nanyang Technological University (NTU), 50 Nanyang Drive, Singapore 637553, Singapore
| |
Collapse
|
49
|
Kulemzina I, Ang K, Zhao X, Teh JT, Verma V, Suranthran S, Chavda AP, Huber RG, Eisenhaber B, Eisenhaber F, Yan J, Ivanov D. A Reversible Association between Smc Coiled Coils Is Regulated by Lysine Acetylation and Is Required for Cohesin Association with the DNA. Mol Cell 2016; 63:1044-54. [PMID: 27618487 DOI: 10.1016/j.molcel.2016.08.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 03/07/2016] [Accepted: 08/05/2016] [Indexed: 12/16/2022]
Abstract
Cohesin is a ring-shaped protein complex that is capable of embracing DNA. Most of the ring circumference is comprised of the anti-parallel intramolecular coiled coils of the Smc1 and Smc3 proteins, which connect globular head and hinge domains. Smc coiled coil arms contain multiple acetylated and ubiquitylated lysines. To investigate the role of these modifications, we substituted lysines for arginines to mimic the unmodified state and uncovered genetic interaction between the Smc arms. Using scanning force microscopy, we show that wild-type Smc arms associate with each other when the complex is not on DNA. Deacetylation of the Smc1/Smc3 dimers promotes arms' dissociation. Smc arginine mutants display loose packing of the Smc arms and, although they dimerize at the hinges, fail to connect the heads and associate with the DNA. Our findings highlight the importance of a "collapsed ring," or "rod," conformation of cohesin for its loading on the chromosomes.
Collapse
MESH Headings
- Acetylation
- Amino Acid Substitution
- Animals
- Arginine/metabolism
- Baculoviridae/genetics
- Baculoviridae/metabolism
- Cell Cycle Proteins/chemistry
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Chromatids/chemistry
- Chromatids/metabolism
- Chromatids/ultrastructure
- Chromosomal Proteins, Non-Histone/chemistry
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- Chromosomes, Fungal/chemistry
- Chromosomes, Fungal/metabolism
- Chromosomes, Fungal/ultrastructure
- Cloning, Molecular
- DNA, Fungal/chemistry
- DNA, Fungal/genetics
- DNA, Fungal/metabolism
- Gene Expression
- Gene Expression Regulation, Fungal
- Lysine/metabolism
- Protein Conformation, alpha-Helical
- Protein Interaction Domains and Motifs
- Protein Processing, Post-Translational
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins/chemistry
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Sf9 Cells
- Signal Transduction
- Spodoptera
- Cohesins
Collapse
Affiliation(s)
- Irina Kulemzina
- Bioinformatics Institute, A(∗)STAR, Singapore 138671, Singapore; Friedrich Miescher Laboratory of the Max Planck Society, Tuebingen 72076, Germany
| | - Keven Ang
- Bioinformatics Institute, A(∗)STAR, Singapore 138671, Singapore
| | - Xiaodan Zhao
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore
| | - Jun-Thing Teh
- Bioinformatics Institute, A(∗)STAR, Singapore 138671, Singapore
| | - Vikash Verma
- Friedrich Miescher Laboratory of the Max Planck Society, Tuebingen 72076, Germany
| | | | - Alap P Chavda
- Bioinformatics Institute, A(∗)STAR, Singapore 138671, Singapore
| | - Roland G Huber
- Bioinformatics Institute, A(∗)STAR, Singapore 138671, Singapore
| | | | - Frank Eisenhaber
- Bioinformatics Institute, A(∗)STAR, Singapore 138671, Singapore; School of Computer Engineering, Nanyang Technological University, Singapore 637553, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117597, Singapore
| | - Jie Yan
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore; Department of Physics, National University of Singapore, Singapore 117551, Singapore; Center for Bioimaging Sciences, National University of Singapore, Singapore 117557, Singapore
| | - Dmitri Ivanov
- Bioinformatics Institute, A(∗)STAR, Singapore 138671, Singapore; Institute of Molecular and Cell Biology, A(∗)STAR, Singapore 138673, Singapore; Friedrich Miescher Laboratory of the Max Planck Society, Tuebingen 72076, Germany; Department of Physics, National University of Singapore, Singapore 117551, Singapore.
| |
Collapse
|
50
|
|