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Sakarika M, Kerckhof FM, Van Peteghem L, Pereira A, Van Den Bossche T, Bouwmeester R, Gabriels R, Van Haver D, Ulčar B, Martens L, Impens F, Boon N, Ganigué R, Rabaey K. The nutritional composition and cell size of microbial biomass for food applications are defined by the growth conditions. Microb Cell Fact 2023; 22:254. [PMID: 38072930 PMCID: PMC10712164 DOI: 10.1186/s12934-023-02265-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 12/02/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND It is increasingly recognized that conventional food production systems are not able to meet the globally increasing protein needs, resulting in overexploitation and depletion of resources, and environmental degradation. In this context, microbial biomass has emerged as a promising sustainable protein alternative. Nevertheless, often no consideration is given on the fact that the cultivation conditions affect the composition of microbial cells, and hence their quality and nutritional value. Apart from the properties and nutritional quality of the produced microbial food (ingredient), this can also impact its sustainability. To qualitatively assess these aspects, here, we investigated the link between substrate availability, growth rate, cell composition and size of Cupriavidus necator and Komagataella phaffii. RESULTS Biomass with decreased nucleic acid and increased protein content was produced at low growth rates. Conversely, high rates resulted in larger cells, which could enable more efficient biomass harvesting. The proteome allocation varied across the different growth rates, with more ribosomal proteins at higher rates, which could potentially affect the techno-functional properties of the biomass. Considering the distinct amino acid profiles established for the different cellular components, variations in their abundance impacts the product quality leading to higher cysteine and phenylalanine content at low growth rates. Therefore, we hint that costly external amino acid supplementations that are often required to meet the nutritional needs could be avoided by carefully applying conditions that enable targeted growth rates. CONCLUSION In summary, we demonstrate tradeoffs between nutritional quality and production rate, and we discuss the microbial biomass properties that vary according to the growth conditions.
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Affiliation(s)
- Myrsini Sakarika
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, Ghent, B-9000, Belgium.
- Center for Advanced Process Technology for Urban Resource recovery (CAPTURE), Frieda Saeysstraat 1, Ghent, 9052, Belgium.
| | - Frederiek-Maarten Kerckhof
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, Ghent, B-9000, Belgium
- Center for Advanced Process Technology for Urban Resource recovery (CAPTURE), Frieda Saeysstraat 1, Ghent, 9052, Belgium
- Kytos BV, IIC UGent, Frieda Saeysstraat 1/B, Ghent, 9052, Belgium
| | - Lotte Van Peteghem
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, Ghent, B-9000, Belgium
- Center for Advanced Process Technology for Urban Resource recovery (CAPTURE), Frieda Saeysstraat 1, Ghent, 9052, Belgium
| | - Alexandra Pereira
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, Ghent, B-9000, Belgium
- Center for Advanced Process Technology for Urban Resource recovery (CAPTURE), Frieda Saeysstraat 1, Ghent, 9052, Belgium
| | - Tim Van Den Bossche
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Robbin Bouwmeester
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Ralf Gabriels
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Delphi Van Haver
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Proteomics Core, VIB, Ghent, Belgium
| | - Barbara Ulčar
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, Ghent, B-9000, Belgium
- Center for Advanced Process Technology for Urban Resource recovery (CAPTURE), Frieda Saeysstraat 1, Ghent, 9052, Belgium
| | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Francis Impens
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Proteomics Core, VIB, Ghent, Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, Ghent, B-9000, Belgium
- Center for Advanced Process Technology for Urban Resource recovery (CAPTURE), Frieda Saeysstraat 1, Ghent, 9052, Belgium
| | - Ramon Ganigué
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, Ghent, B-9000, Belgium
- Center for Advanced Process Technology for Urban Resource recovery (CAPTURE), Frieda Saeysstraat 1, Ghent, 9052, Belgium
| | - Korneel Rabaey
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, Ghent, B-9000, Belgium
- Center for Advanced Process Technology for Urban Resource recovery (CAPTURE), Frieda Saeysstraat 1, Ghent, 9052, Belgium
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2
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Sahoo BR, Bardwell JCA. SERF, a family of tiny highly conserved, highly charged proteins with enigmatic functions. FEBS J 2023; 290:4150-4162. [PMID: 35694898 DOI: 10.1111/febs.16555] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 06/07/2022] [Accepted: 06/10/2022] [Indexed: 11/27/2022]
Abstract
Amyloid formation is a misfolding process that has been linked to age-related diseases, including Alzheimer's and Huntington's. Understanding how cellular factors affect this process in vivo is vital in realizing the dream of controlling this insidious process that robs so many people of their humanity. SERF (small EDRK-rich factor) was initially isolated as a factor that accelerated polyglutamine amyloid formation in a C. elegans model. SERF knockouts inhibit amyloid formation of a number of proteins that include huntingtin, α-synuclein and β-amyloid which are associated with Huntington's, Parkinson's and Alzheimer's disease, respectively, and purified SERF protein speeds their amyloid formation in vitro. SERF proteins are highly conserved, highly charged and conformationally dynamic proteins that form a fuzzy complex with amyloid precursors. They appear to act by specifically accelerating the primary step of amyloid nucleation. Brain-specific SERF knockout mice, though viable, appear to be more prone to deposition of amyloids, and show modified fibril morphology. Whole-body knockouts are perinatally lethal due to an apparently unrelated developmental issue. Recently, it was found that SERF binds RNA and is localized to nucleic acid-rich membraneless compartments. SERF-related sequences are commonly found fused to zinc finger sequences. These results point towards a nucleic acid-binding function. How this function relates to their ability to accelerate amyloid formation is currently obscure. In this review, we discuss the possible biological functions of SERF family proteins in the context of their structural fuzziness, modulation of amyloid pathway, nucleic acid binding and their fusion to folded proteins.
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Affiliation(s)
- Bikash R Sahoo
- Department of Molecular, Cellular and Developmental Biology, Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
| | - James C A Bardwell
- Department of Molecular, Cellular and Developmental Biology, Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
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3
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van den Elzen A, Helena-Bueno K, Brown CR, Chan LI, Melnikov S. Ribosomal proteins can hold a more accurate record of bacterial thermal adaptation compared to rRNA. Nucleic Acids Res 2023; 51:8048-8059. [PMID: 37395434 PMCID: PMC10450194 DOI: 10.1093/nar/gkad560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 05/29/2023] [Accepted: 06/19/2023] [Indexed: 07/04/2023] Open
Abstract
Ribosomal genes are widely used as 'molecular clocks' to infer evolutionary relationships between species. However, their utility as 'molecular thermometers' for estimating optimal growth temperature of microorganisms remains uncertain. Previously, some estimations were made using the nucleotide composition of ribosomal RNA (rRNA), but the universal application of this approach was hindered by numerous outliers. In this study, we aimed to address this problem by identifying additional indicators of thermal adaptation within the sequences of ribosomal proteins. By comparing sequences from 2021 bacteria with known optimal growth temperature, we identified novel indicators among the metal-binding residues of ribosomal proteins. We found that these residues serve as conserved adaptive features for bacteria thriving above 40°C, but not at lower temperatures. Furthermore, the presence of these metal-binding residues exhibited a stronger correlation with the optimal growth temperature of bacteria compared to the commonly used correlation with the 16S rRNA GC content. And an even more accurate correlation was observed between the optimal growth temperature and the YVIWREL amino acid content within ribosomal proteins. Overall, our work suggests that ribosomal proteins contain a more accurate record of bacterial thermal adaptation compared to rRNA. This finding may simplify the analysis of unculturable and extinct species.
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Affiliation(s)
| | - Karla Helena-Bueno
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Charlotte R Brown
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Lewis I Chan
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Sergey V Melnikov
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
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The Structure of Evolutionary Model Space for Proteins across the Tree of Life. BIOLOGY 2023; 12:biology12020282. [PMID: 36829559 PMCID: PMC9952988 DOI: 10.3390/biology12020282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/04/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023]
Abstract
The factors that determine the relative rates of amino acid substitution during protein evolution are complex and known to vary among taxa. We estimated relative exchangeabilities for pairs of amino acids from clades spread across the tree of life and assessed the historical signal in the distances among these clade-specific models. We separately trained these models on collections of arbitrarily selected protein alignments and on ribosomal protein alignments. In both cases, we found a clear separation between the models trained using multiple sequence alignments from bacterial clades and the models trained on archaeal and eukaryotic data. We assessed the predictive power of our novel clade-specific models of sequence evolution by asking whether fit to the models could be used to identify the source of multiple sequence alignments. Model fit was generally able to correctly classify protein alignments at the level of domain (bacterial versus archaeal), but the accuracy of classification at finer scales was much lower. The only exceptions to this were the relatively high classification accuracy for two archaeal lineages: Halobacteriaceae and Thermoprotei. Genomic GC content had a modest impact on relative exchangeabilities despite having a large impact on amino acid frequencies. Relative exchangeabilities involving aromatic residues exhibited the largest differences among models. There were a small number of exchangeabilities that exhibited large differences in comparisons among major clades and between generalized models and ribosomal protein models. Taken as a whole, these results reveal that a small number of relative exchangeabilities are responsible for much of the structure of the "model space" for protein sequence evolution. The clade-specific models we generated may be useful tools for protein phylogenetics, and the structure of evolutionary model space that they revealed has implications for phylogenomic inference across the tree of life.
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5
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Patel S, Howard D, Chowdhury N, Derieux C, Wellslager B, Yilmaz Ö, French L. Characterization of Human Genes Modulated by Porphyromonas gingivalis Highlights the Ribosome, Hypothalamus, and Cholinergic Neurons. Front Immunol 2021; 12:646259. [PMID: 34194426 PMCID: PMC8236716 DOI: 10.3389/fimmu.2021.646259] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 05/20/2021] [Indexed: 12/12/2022] Open
Abstract
Porphyromonas gingivalis, a bacterium associated with periodontal disease, is a suspected cause of Alzheimer's disease. This bacterium is reliant on gingipain proteases, which cleave host proteins after arginine and lysine residues. To characterize gingipain susceptibility, we performed enrichment analyses of arginine and lysine proportion proteome-wide. Genes differentially expressed in brain samples with detected P. gingivalis reads were also examined. Genes from these analyses were tested for functional enrichment and specific neuroanatomical expression patterns. Proteins in the SRP-dependent cotranslational protein targeting to membrane pathway were enriched for these residues and previously associated with periodontal and Alzheimer's disease. These ribosomal genes are up-regulated in prefrontal cortex samples with detected P. gingivalis sequences. Other differentially expressed genes have been previously associated with dementia (ITM2B, MAPT, ZNF267, and DHX37). For an anatomical perspective, we characterized the expression of the P. gingivalis associated genes in the mouse and human brain. This analysis highlighted the hypothalamus, cholinergic neurons, and the basal forebrain. Our results suggest markers of neural P. gingivalis infection and link the cholinergic and gingipain hypotheses of Alzheimer's disease.
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Affiliation(s)
- Sejal Patel
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Derek Howard
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Nityananda Chowdhury
- Department of Oral Health Sciences, Medical University of South Carolina, Charleston, SC, United States
| | - Casey Derieux
- Department of Oral Health Sciences, Medical University of South Carolina, Charleston, SC, United States
| | - Bridgette Wellslager
- Department of Oral Health Sciences, Medical University of South Carolina, Charleston, SC, United States
| | - Özlem Yilmaz
- Department of Oral Health Sciences, Medical University of South Carolina, Charleston, SC, United States
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC, United States
| | - Leon French
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
- Institute for Medical Science, University of Toronto, Toronto, ON, Canada
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6
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Zhao L, Castanié-Cornet MP, Kumar S, Genevaux P, Hayer-Hartl M, Hartl FU. Bacterial RF3 senses chaperone function in co-translational folding. Mol Cell 2021; 81:2914-2928.e7. [PMID: 34107307 DOI: 10.1016/j.molcel.2021.05.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 04/05/2021] [Accepted: 05/13/2021] [Indexed: 10/21/2022]
Abstract
Molecular chaperones assist with protein folding by interacting with nascent polypeptide chains (NCs) during translation. Whether the ribosome can sense chaperone defects and, in response, abort translation of misfolding NCs has not yet been explored. Here we used quantitative proteomics to investigate the ribosome-associated chaperone network in E. coli and the consequences of its dysfunction. Trigger factor and the DnaK (Hsp70) system are the major NC-binding chaperones. HtpG (Hsp90), GroEL, and ClpB contribute increasingly when DnaK is deficient. Surprisingly, misfolding because of defects in co-translational chaperone function or amino acid analog incorporation results in recruitment of the non-canonical release factor RF3. RF3 recognizes aberrant NCs and then moves to the peptidyltransferase site to cooperate with RF2 in mediating chain termination, facilitating clearance by degradation. This function of RF3 reduces the accumulation of misfolded proteins and is critical for proteostasis maintenance and cell survival under conditions of limited chaperone availability.
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Affiliation(s)
- Liang Zhao
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Marie-Pierre Castanié-Cornet
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062 Toulouse, France
| | - Sneha Kumar
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Pierre Genevaux
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062 Toulouse, France
| | - Manajit Hayer-Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
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7
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Chang RL, Stanley JA, Robinson MC, Sher JW, Li Z, Chan YA, Omdahl AR, Wattiez R, Godzik A, Matallana-Surget S. Protein structure, amino acid composition and sequence determine proteome vulnerability to oxidation-induced damage. EMBO J 2020; 39:e104523. [PMID: 33073387 PMCID: PMC7705453 DOI: 10.15252/embj.2020104523] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 09/16/2020] [Accepted: 09/22/2020] [Indexed: 02/05/2023] Open
Abstract
Oxidative stress alters cell viability, from microorganism irradiation sensitivity to human aging and neurodegeneration. Deleterious effects of protein carbonylation by reactive oxygen species (ROS) make understanding molecular properties determining ROS susceptibility essential. The radiation‐resistant bacterium Deinococcus radiodurans accumulates less carbonylation than sensitive organisms, making it a key model for deciphering properties governing oxidative stress resistance. We integrated shotgun redox proteomics, structural systems biology, and machine learning to resolve properties determining protein damage by γ‐irradiation in Escherichia coli and D. radiodurans at multiple scales. Local accessibility, charge, and lysine enrichment accurately predict ROS susceptibility. Lysine, methionine, and cysteine usage also contribute to ROS resistance of the D. radiodurans proteome. Our model predicts proteome maintenance machinery, and proteins protecting against ROS are more resistant in D. radiodurans. Our findings substantiate that protein‐intrinsic protection impacts oxidative stress resistance, identifying causal molecular properties.
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Affiliation(s)
- Roger L Chang
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Julian A Stanley
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA, USA
| | - Matthew C Robinson
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA, USA
| | - Joel W Sher
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA, USA
| | - Zhanwen Li
- Division of Biomedical Sciences, University of California Riverside School of Medicine, Riverside, CA, USA
| | - Yujia A Chan
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Ashton R Omdahl
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA, USA
| | - Ruddy Wattiez
- Department of Proteomics and Microbiology, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Adam Godzik
- Division of Biomedical Sciences, University of California Riverside School of Medicine, Riverside, CA, USA
| | - Sabine Matallana-Surget
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, UK
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8
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Ancestral function of Inhibitors-of-kappaB regulates Caenorhabditis elegans development. Sci Rep 2020; 10:16153. [PMID: 32999373 PMCID: PMC7527347 DOI: 10.1038/s41598-020-73146-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 09/10/2020] [Indexed: 01/08/2023] Open
Abstract
Mammalian IκB proteins (IκBs) exert their main function as negative regulators of NF-κB, a central signaling pathway controlling immunity and inflammation. An alternative chromatin role for IκBs has been shown to affect stemness and cell differentiation. However, the involvement of NF-κB in this function has not been excluded. NFKI-1 and IKB-1 are IκB homologs in Caenorhabditis elegans, which lacks NF-κB nuclear effectors. We found that nfki-1 and ikb-1 mutants display developmental defects that phenocopy mutations in Polycomb and UTX-1 histone demethylase, suggesting a role for C. elegans IκBs in chromatin regulation. Further supporting this possibility (1) we detected NFKI-1 in the nucleus of cells; (2) NFKI-1 and IKB-1 bind to histones and Polycomb proteins, (3) and associate with chromatin in vivo, and (4) mutations in nfki-1 and ikb-1 alter chromatin marks. Based on these results, we propose that ancestral IκB inhibitors modulate Polycomb activity at specific gene subsets with an impact on development.
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Petelski AA, Slavov N. Analyzing Ribosome Remodeling in Health and Disease. Proteomics 2020; 20:e2000039. [PMID: 32820594 PMCID: PMC7501214 DOI: 10.1002/pmic.202000039] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/01/2020] [Indexed: 12/24/2022]
Abstract
Increasing evidence suggests that ribosomes actively regulate protein synthesis. However, much of this evidence is indirect, leaving this layer of gene regulation largely unexplored, in part due to methodological limitations. Indeed, evidence is reviewed demonstrating that commonly used methods, such as transcriptomics, are inadequate because the variability in mRNAs coding for ribosomal proteins (RP) does not necessarily correspond to RP variability. Thus protein remodeling of ribosomes should be investigated by methods that allow direct quantification of RPs, ideally of isolated ribosomes. Such methods are reviewed, focusing on mass spectrometry and emphasizing method-specific biases and approaches to control these biases. It is argued that using multiple complementary methods can help reduce the danger of interpreting reproducible systematic biases as evidence for ribosome remodeling.
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Affiliation(s)
- Aleksandra A Petelski
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, USA
- Barnett Institute, Northeastern University, Boston, MA, 02115, USA
- Department of Biology, Northeastern University, Boston, MA, 02115, USA
| | - Nikolai Slavov
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, USA
- Barnett Institute, Northeastern University, Boston, MA, 02115, USA
- Department of Biology, Northeastern University, Boston, MA, 02115, USA
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10
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Bozorgmehr JH. The origin of chromosomal histones in a 30S ribosomal protein. Gene 2020; 726:144155. [PMID: 31629821 DOI: 10.1016/j.gene.2019.144155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 10/01/2019] [Accepted: 10/03/2019] [Indexed: 11/18/2022]
Abstract
Histones are genes that regulate chromatin structure. They are present in both eukaryotes and archaea, and form nucleosomes with DNA, but their exact evolutionary origins have hitherto remained a mystery. A longstanding hypothesis is that they have precursors in ribosomal proteins with whom they share much in common in terms of size and chemistry. By examining the proteome of the Asgard archaeon, Lokiarchaeum, the most conserved of all the histones, H4, is found to plausibly be homologous with one of its 30S ribosomal proteins, RPS6. This is based on both sequence identity and statistical analysis. The N-terminal tail, containing key sites involved in post-translational modifications, is notably present in the precursor gene. Although other archaeal groups possess similar homologs, these are not as close to H4 as the one found in Lokiarchaeum. The other core histones, H2A, H2B and H3, appear to have also evolved from the same ribosomal protein. Parts of H4 are also similar to another ribosomal protein, namely RPS15, suggesting that the ancestral precursor could have resembled both. Eukaryotic histones, in addition, appear to have an independent origin to that of their archaeal counterparts that evolved from similar, but still different, 30S subunit proteins, some of which are much more like histones in terms of their physical structure. The nucleosome may, therefore, be not only of archaeal but also of ribosomal origin.
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11
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Thangaraj S, Giordano M, Sun J. Comparative Proteomic Analysis Reveals New Insights Into the Common and Specific Metabolic Regulation of the Diatom Skeletonema dohrnii to the Silicate and Temperature Availability. FRONTIERS IN PLANT SCIENCE 2020; 11:578915. [PMID: 33224167 PMCID: PMC7674209 DOI: 10.3389/fpls.2020.578915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/28/2020] [Indexed: 05/12/2023]
Abstract
Silicate (Si) and temperature are essential drivers for diatom growth and development in the ocean. Response of diatoms to these particular stress has been investigated; however, their common and specific responses to regulate intracellular development and growth are not known. Here, we investigated the combination of physiological characteristics and comparative proteomics of the diatom Skeletonema dohrnii grown in silicate- and temperature-limited conditions. Results show that cell carbon and lipid quotas were higher at lower-temperature cells, whereas cellular phosphate was higher in cells grown with lower Si. In silicate-limited cells, nitrate transporters were downregulated and resulted in lower nitrate assimilation, whereas the phosphate transporters and its assimilation were reduced in lower-temperature conditions. In photosynthesis, lower silicate caused impact in the linear electron flow and NADPH production, whereas cycling electron transport and ATP production were affected by the lower temperature. Concerning cell cycle, imbalances in the translation process were observed in lower-silicate cells, whereas impact in the transcription mechanism was observed in lower-temperature cells. However, proteins associated with carbon fixation and photorespiration were downregulated in both stress conditions, while the carbohydrate and lipid synthesis proteins were upregulated. Our results showed new insights into the common and specific responses on the proteome and physiology of S. dohrnii to silicate and temperature limitation, providing particular nutrient (Si)- and temperature-dependent mechanisms in diatoms.
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Affiliation(s)
- Satheeswaran Thangaraj
- College of Marine Science and Technology, China University of Geosciences (Wuhan), Wuhan, China
| | - Mario Giordano
- Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Jun Sun
- College of Marine Science and Technology, China University of Geosciences (Wuhan), Wuhan, China
- *Correspondence: Jun Sun,
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12
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Dao Duc K, Batra SS, Bhattacharya N, Cate JHD, Song YS. Differences in the path to exit the ribosome across the three domains of life. Nucleic Acids Res 2019; 47:4198-4210. [PMID: 30805621 PMCID: PMC6486554 DOI: 10.1093/nar/gkz106] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 02/22/2019] [Indexed: 01/07/2023] Open
Abstract
The ribosome exit tunnel is an important structure involved in the regulation of translation and other essential functions such as protein folding. By comparing 20 recently obtained cryo-EM and X-ray crystallography structures of the ribosome from all three domains of life, we here characterize the key similarities and differences of the tunnel across species. We first show that a hierarchical clustering of tunnel shapes closely reflects the species phylogeny. Then, by analyzing the ribosomal RNAs and proteins, we explain the observed geometric variations and show direct association between the conservations of the geometry, structure and sequence. We find that the tunnel is more conserved in the upper part close to the polypeptide transferase center, while in the lower part, it is substantially narrower in eukaryotes than in bacteria. Furthermore, we provide evidence for the existence of a second constriction site in eukaryotic exit tunnels. Overall, these results have several evolutionary and functional implications, which explain certain differences between eukaryotes and prokaryotes in their translation mechanisms. In particular, they suggest that major co-translational functions of bacterial tunnels were externalized in eukaryotes, while reducing the tunnel size provided some other advantages, such as facilitating the nascent chain elongation and enabling antibiotic resistance.
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Affiliation(s)
- Khanh Dao Duc
- Computer Science Division, University of California, Berkeley, CA 94720, USA
| | - Sanjit S Batra
- Computer Science Division, University of California, Berkeley, CA 94720, USA
| | | | - Jamie H D Cate
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.,Department of Chemistry, University of California, Berkeley, CA 94720, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yun S Song
- Computer Science Division, University of California, Berkeley, CA 94720, USA.,Department of Statistics, University of California, Berkeley, CA 94720, USA.,Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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13
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Protein synthesis rates and ribosome occupancies reveal determinants of translation elongation rates. Proc Natl Acad Sci U S A 2019; 116:15023-15032. [PMID: 31292258 PMCID: PMC6660795 DOI: 10.1073/pnas.1817299116] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Although protein synthesis dynamics has been studied both with theoretical models and by profiling ribosome footprints, the determinants of ribosome flux along open reading frames (ORFs) are not fully understood. Combining measurements of protein synthesis rate with ribosome footprinting data, we here inferred translation initiation and elongation rates for over a 1,000 ORFs in exponentially growing wild-type yeast cells. We found that the amino acid composition of synthesized proteins is as important a determinant of translation elongation rate as parameters related to codon and transfer RNA (tRNA) adaptation. We did not find evidence of ribosome collisions curbing the protein output of yeast transcripts, either in high translation conditions associated with exponential growth, or in strains in which deletion of individual ribosomal protein (RP) genes leads to globally increased or decreased translation. Slow translation elongation is characteristic of RP-encoding transcripts, which have markedly lower protein output compared with other transcripts with equally high ribosome densities.
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14
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Correddu D, Montaño López JDJ, Vadakkedath PG, Lai A, Pernes JI, Watson PR, Leung IKH. An improved method for the heterologous production of soluble human ribosomal proteins in Escherichia coli. Sci Rep 2019; 9:8884. [PMID: 31222068 PMCID: PMC6586885 DOI: 10.1038/s41598-019-45323-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 05/31/2019] [Indexed: 11/11/2022] Open
Abstract
Human ribosomal proteins play important structural and functional roles in the ribosome and in protein synthesis. An efficient method to recombinantly produce and purify these proteins would enable their full characterisation. However, the production of human ribosomal proteins can be challenging. The only published method about the recombinant production of human ribosomal proteins involved the recovery of proteins from inclusion bodies, a process that is tedious and may lead to significant loss of yield. Herein, we explored the use of different Escherichia coli competent cells and fusion protein tags for the recombinant production of human ribosomal proteins. We found that, by using thioredoxin as a fusion protein, soluble ribosomal protein could be obtained directly from cell lysates, thus leading to an improved method to recombinantly produce these proteins.
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Affiliation(s)
- Danilo Correddu
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand
| | - José de Jesús Montaño López
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand.,Facultad de Ingeniería, Universidad Nacional Autónoma de México, Av. Universidad 3000, Ciudad Universitaria, Coyoacán, Cd. Mx., CP 04510, Mexico
| | - Praveen G Vadakkedath
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand.,The MacDiarmid Institute for Advanced Materials and Nanotechnology, Victoria University of Wellington, PO Box 600, Wellington, 6140, New Zealand
| | - Amy Lai
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand
| | - Jane I Pernes
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand.,School of Cellular and Molecular Medicine, University of Bristol, Biomedical Sciences Building, University Walk, Bristol, BS8 1TD, United Kingdom
| | - Paris R Watson
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand.,School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, 6140, New Zealand
| | - Ivanhoe K H Leung
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand. .,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand.
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15
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Wu Y, Wu P, Wang B, Shao ZQ. Genome-Wide Analysis Reveals Ancestral Lack of Seventeen Different tRNAs and Clade-Specific Loss of tRNA-CNNs in Archaea. Front Microbiol 2018; 9:1245. [PMID: 29930548 PMCID: PMC6000648 DOI: 10.3389/fmicb.2018.01245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Accepted: 05/23/2018] [Indexed: 12/02/2022] Open
Abstract
Transfer RNA (tRNA) is a category of RNAs that specifically decode messenger RNAs (mRNAs) into proteins by recognizing a set of 61 codons commonly adopted by different life domains. The composition and abundance of tRNAs play critical roles in shaping codon usage and pairing bias, which subsequently modulate mRNA translation efficiency and accuracy. Over the past few decades, effort has been concentrated on evaluating the specificity and redundancy of different tRNA families. However, the mechanism and processes underlying tRNA evolution have only rarely been investigated. In this study, by surveying tRNA genes in 167 completely sequenced genomes, we systematically investigated the composition and evolution of tRNAs in Archaea from a phylogenetic perspective. Our data revealed that archaeal genomes are compact in both tRNA types and copy number. Generally, no more than 44 different types of tRNA are present in archaeal genomes to decode the 61 canonical codons, and most of them have only one gene copy per genome. Among them, tRNA-Met was significantly overrepresented, with an average of three copies per genome. In contrast, the tRNA-UAU and 16 tRNAs with A-starting anticodons (tRNA-ANNs) were rarely detected in all archaeal genomes. The conspicuous absence of these tRNAs across the archaeal phylogeny suggests they might have not been evolved in the common ancestor of Archaea, rather than have lost independently from different clades. Furthermore, widespread absence of tRNA-CNNs in the Methanococcales and Methanobacteriales genomes indicates convergent loss of these tRNAs in the two clades. This clade-specific tRNA loss may be attributing to the reductive evolution of their genomes. Our data suggest that the current tRNA profiles in Archaea are contributed not only by the ancestral tRNA composition, but also by differential maintenance and loss of redundant tRNAs.
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Affiliation(s)
- Yue Wu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China.,Institute of Bioinformatics, University of Georgia, Athens, GA, United States
| | - Ping Wu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Bin Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Zhu-Qing Shao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
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16
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Zanello P. The competition between chemistry and biology in assembling iron–sulfur derivatives. Molecular structures and electrochemistry. Part V. {[Fe4S4](SCysγ)4} proteins. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2016.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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