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Hu SK, Anderson RE, Pachiadaki MG, Edgcomb VP, Serres MH, Sylva SP, German CR, Seewald JS, Lang SQ, Huber JA. Microbial eukaryotic predation pressure and biomass at deep-sea hydrothermal vents. ISME J 2024; 18:wrae004. [PMID: 38366040 PMCID: PMC10939315 DOI: 10.1093/ismejo/wrae004] [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] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/22/2023] [Accepted: 01/12/2024] [Indexed: 02/18/2024]
Abstract
Deep-sea hydrothermal vent geochemistry shapes the foundation of the microbial food web by fueling chemolithoautotrophic microbial activity. Microbial eukaryotes (or protists) play a critical role in hydrothermal vent food webs as consumers and hosts of symbiotic bacteria, and as a nutritional source to higher trophic levels. We measured microbial eukaryotic cell abundance and predation pressure in low-temperature diffuse hydrothermal fluids at the Von Damm and Piccard vent fields along the Mid-Cayman Rise in the Western Caribbean Sea. We present findings from experiments performed under in situ pressure that show cell abundances and grazing rates higher than those done at 1 atmosphere (shipboard ambient pressure); this trend was attributed to the impact of depressurization on cell integrity. A relationship between the protistan grazing rate, prey cell abundance, and temperature of end-member hydrothermal vent fluid was observed at both vent fields, regardless of experimental approach. Our results show substantial protistan biomass at hydrothermally fueled microbial food webs, and when coupled with improved grazing estimates, suggest an important contribution of grazers to the local carbon export and supply of nutrient resources to the deep ocean.
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Affiliation(s)
- Sarah K Hu
- Department of Oceanography, Texas A&M University, College Station, TX 77843, United States
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
| | - Rika E Anderson
- Biology Department, Carleton College, Northfield, MN 55057, United States
| | - Maria G Pachiadaki
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
| | - Virginia P Edgcomb
- Department of Geology & Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
| | - Margrethe H Serres
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
| | - Sean P Sylva
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
| | - Christopher R German
- Department of Geology & Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
| | - Jeffrey S Seewald
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
| | - Susan Q Lang
- Department of Geology & Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
| | - Julie A Huber
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
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Ong WK, Vu TT, Lovendahl KN, Llull JM, Serres MH, Romine MF, Reed JL. Comparisons of Shewanella strains based on genome annotations, modeling, and experiments. BMC Syst Biol 2014; 8:31. [PMID: 24621294 PMCID: PMC4007644 DOI: 10.1186/1752-0509-8-31] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 03/06/2014] [Indexed: 01/19/2023]
Abstract
BACKGROUND Shewanella is a genus of facultatively anaerobic, Gram-negative bacteria that have highly adaptable metabolism which allows them to thrive in diverse environments. This quality makes them an attractive bacterial target for research in bioremediation and microbial fuel cell applications. Constraint-based modeling is a useful tool for helping researchers gain insights into the metabolic capabilities of these bacteria. However, Shewanella oneidensis MR-1 is the only strain with a genome-scale metabolic model constructed out of 21 sequenced Shewanella strains. RESULTS In this work, we updated the model for Shewanella oneidensis MR-1 and constructed metabolic models for three other strains, namely Shewanella sp. MR-4, Shewanella sp. W3-18-1, and Shewanella denitrificans OS217 which span the genus based on the number of genes lost in comparison to MR-1. We also constructed a Shewanella core model that contains the genes shared by all 21 sequenced strains and a few non-conserved genes associated with essential reactions. Model comparisons between the five constructed models were done at two levels - for wildtype strains under different growth conditions and for knockout mutants under the same growth condition. In the first level, growth/no-growth phenotypes were predicted by the models on various carbon sources and electron acceptors. Cluster analysis of these results revealed that the MR-1 model is most similar to the W3-18-1 model, followed by the MR-4 and OS217 models when considering predicted growth phenotypes. However, a cluster analysis done based on metabolic gene content revealed that the MR-4 and W3-18-1 models are the most similar, with the MR-1 and OS217 models being more distinct from these latter two strains. As a second level of comparison, we identified differences in reaction and gene content which give rise to different functional predictions of single and double gene knockout mutants using Comparison of Networks by Gene Alignment (CONGA). Here, we showed how CONGA can be used to find biomass, metabolic, and genetic differences between models. CONCLUSIONS We developed four strain-specific models and a general core model that can be used to do various in silico studies of Shewanella metabolism. The developed models provide a platform for a systematic investigation of Shewanella metabolism to aid researchers using Shewanella in various biotechnology applications.
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Sadler NC, Melnicki MR, Serres MH, Merkley ED, Chrisler WB, Hill EA, Romine MF, Kim S, Zink EM, Datta S, Smith RD, Beliaev AS, Konopka A, Wright AT. Live cell chemical profiling of temporal redox dynamics in a photoautotrophic cyanobacterium. ACS Chem Biol 2014; 9:291-300. [PMID: 24168666 DOI: 10.1021/cb400769v] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Protein reduction-oxidation (redox) modification is an important mechanism that allows microorganisms to sense environmental changes and initiate cellular responses. We have developed a quantitative chemical probe approach for live cell labeling and imaging of proteins that are sensitive to redox modifications. We utilize this in vivo strategy to identify 176 proteins undergoing ∼5-10-fold dynamic redox change in response to nutrient limitation and subsequent replenishment in the photoautotrophic cyanobacterium Synechococcus sp. PCC 7002. We detect redox changes in as little as 30 s after nutrient perturbation and oscillations in reduction and oxidation for 60 min following the perturbation. Many of the proteins undergoing dynamic redox transformations participate in the major components for the production (photosystems and electron transport chains) or consumption (Calvin-Benson cycle and protein synthesis) of reductant and/or energy in photosynthetic organisms. Thus, our in vivo approach reveals new redox-susceptible proteins and validates those previously identified in vitro.
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Affiliation(s)
- Natalie C. Sadler
- Biological
Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Matthew R. Melnicki
- Biological
Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Margrethe H. Serres
- Bay
Paul Center, Marine Biological Laboratory, Woods Hole, Massachussetts 02543, United States
| | - Eric D. Merkley
- Biological
Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - William B. Chrisler
- Biological
Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Eric A. Hill
- Biological
Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Margaret F. Romine
- Biological
Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Sangtae Kim
- Biological
Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Erika M. Zink
- Biological
Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Suchitra Datta
- Biological
Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Richard D. Smith
- Biological
Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Alexander S. Beliaev
- Biological
Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Allan Konopka
- Biological
Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Aaron T. Wright
- Biological
Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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4
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Taylor RC, Webb Robertson BJM, Markillie LM, Serres MH, Linggi BE, Aldrich JT, Hill EA, Romine MF, Lipton MS, Wiley HS. Changes in translational efficiency is a dominant regulatory mechanism in the environmental response of bacteria. Integr Biol (Camb) 2013; 5:1393-406. [PMID: 24081429 DOI: 10.1039/c3ib40120k] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To understand how cell physiological state affects mRNA translation, we used Shewanella oneidensis MR-1 grown under steady state conditions at either 20% or 8.5% O2. Using a combination of quantitative proteomics and RNA-Seq, we generated high-confidence data on >1000 mRNA and protein pairs. By using a steady state model, we found that differences in protein-mRNA ratios were primarily due to differences in the translational efficiency of specific genes. When oxygen levels were lowered, 28% of the proteins showed at least a 2-fold change in expression. Transcription levels were sp. significantly altered for 26% of the protein changes; translational efficiency was significantly altered for 46% and a combination of both was responsible for the remaining 28%. Changes in translational efficiency were significantly correlated with the codon usage pattern of the genes and measurable tRNA pools changed in response to altered O2 levels. Our results suggest that changes in the translational efficiency of proteins, in part due to altered tRNA pools, is a major determinant of regulated alterations in protein expression levels in bacteria.
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Affiliation(s)
- Ronald C Taylor
- Computational Biosciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
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5
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Beg QK, Zampieri M, Klitgord N, Collins SB, Altafini C, Serres MH, Segrè D. Detection of transcriptional triggers in the dynamics of microbial growth: application to the respiratorily versatile bacterium Shewanella oneidensis. Nucleic Acids Res 2012; 40:7132-49. [PMID: 22638572 PMCID: PMC3424579 DOI: 10.1093/nar/gks467] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [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] [Indexed: 11/25/2022] Open
Abstract
The capacity of microorganisms to respond to variable external conditions requires a coordination of environment-sensing mechanisms and decision-making regulatory circuits. Here, we seek to understand the interplay between these two processes by combining high-throughput measurement of time-dependent mRNA profiles with a novel computational approach that searches for key genetic triggers of transcriptional changes. Our approach helped us understand the regulatory strategies of a respiratorily versatile bacterium with promising bioenergy and bioremediation applications, Shewanella oneidensis, in minimal and rich media. By comparing expression profiles across these two conditions, we unveiled components of the transcriptional program that depend mainly on the growth phase. Conversely, by integrating our time-dependent data with a previously available large compendium of static perturbation responses, we identified transcriptional changes that cannot be explained solely by internal network dynamics, but are rather triggered by specific genes acting as key mediators of an environment-dependent response. These transcriptional triggers include known and novel regulators that respond to carbon, nitrogen and oxygen limitation. Our analysis suggests a sequence of physiological responses, including a coupling between nitrogen depletion and glycogen storage, partially recapitulated through dynamic flux balance analysis, and experimentally confirmed by metabolite measurements. Our approach is broadly applicable to other systems.
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Affiliation(s)
- Qasim K Beg
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
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Karpinets TV, Romine MF, Schmoyer DD, Kora GH, Syed MH, Leuze MR, Serres MH, Park BH, Samatova NF, Uberbacher EC. Shewanella knowledgebase: integration of the experimental data and computational predictions suggests a biological role for transcription of intergenic regions. Database (Oxford) 2010; 2010:baq012. [PMID: 20627862 PMCID: PMC2911847 DOI: 10.1093/database/baq012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Shewanellae are facultative γ-proteobacteria whose remarkable respiratory versatility has resulted in interest in their utility for bioremediation of heavy metals and radionuclides and for energy generation in microbial fuel cells. Extensive experimental efforts over the last several years and the availability of 21 sequenced Shewanella genomes made it possible to collect and integrate a wealth of information on the genus into one public resource providing new avenues for making biological discoveries and for developing a system level understanding of the cellular processes. The Shewanella knowledgebase was established in 2005 to provide a framework for integrated genome-based studies on Shewanella ecophysiology. The present version of the knowledgebase provides access to a diverse set of experimental and genomic data along with tools for curation of genome annotations and visualization and integration of genomic data with experimental data. As a demonstration of the utility of this resource, we examined a single microarray data set from Shewanella oneidensis MR-1 for new insights into regulatory processes. The integrated analysis of the data predicted a new type of bacterial transcriptional regulation involving co-transcription of the intergenic region with the downstream gene and suggested a biological role for co-transcription that likely prevents the binding of a regulator of the upstream gene to the regulator binding site located in the intergenic region. Database URL:http://shewanella-knowledgebase.org:8080/Shewanella/ or http://spruce.ornl.gov:8080/Shewanella/
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Abstract
BACKGROUND Sequence related families of genes and proteins are common in bacterial genomes. In Escherichia coli they constitute over half of the genome. The presence of families and superfamilies of proteins suggest a history of gene duplication and divergence during evolution. Genome encoded protein families, their size and functional composition, reflect metabolic potentials of the organisms they are found in. Comparing protein families of different organisms give insight into functional differences and similarities. RESULTS Equivalent enzyme families with metabolic functions were selected from the genomes of four experimentally characterized bacteria belonging to separate genera. Both similarities and differences were detected in the protein family memberships, with more similarities being detected among the more closely related organisms. Protein family memberships reflected known metabolic characteristics of the organisms. Differences in divergence of functionally characterized enzyme family members accounted for characteristics of taxa known to differ in those biochemical properties and capabilities. While some members of the gene families will have been acquired by lateral exchange and other former family members will have been lost over time, duplication and divergence of genes and functions appear to have been a significant contributor to the functional diversity of today's microbes. CONCLUSIONS Protein families seem likely to have arisen during evolution by gene duplication and divergence where the gene copies that have been retained are the variants that have led to distinct bacterial physiologies and taxa. Thus divergence of the duplicate enzymes has been a major process in the generation of different kinds of bacteria.
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Affiliation(s)
- Margrethe H Serres
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA.
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Karpinets TV, Obraztsova AY, Wang Y, Schmoyer DD, Kora GH, Park BH, Serres MH, Romine MF, Land ML, Kothe TB, Fredrickson JK, Nealson KH, Uberbacher EC. Conserved synteny at the protein family level reveals genes underlying Shewanella species' cold tolerance and predicts their novel phenotypes. Funct Integr Genomics 2009; 10:97-110. [PMID: 19802638 PMCID: PMC2834769 DOI: 10.1007/s10142-009-0142-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [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: 05/28/2009] [Revised: 08/24/2009] [Accepted: 09/10/2009] [Indexed: 01/26/2023]
Abstract
Bacteria of the genus Shewanella can thrive in different environments and demonstrate significant variability in their metabolic and ecophysiological capabilities including cold and salt tolerance. Genomic characteristics underlying this variability across species are largely unknown. In this study, we address the problem by a comparison of the physiological, metabolic, and genomic characteristics of 19 sequenced Shewanella species. We have employed two novel approaches based on association of a phenotypic trait with the number of the trait-specific protein families (Pfam domains) and on the conservation of synteny (order in the genome) of the trait-related genes. Our first approach is top-down and involves experimental evaluation and quantification of the species’ cold tolerance followed by identification of the correlated Pfam domains and genes with a conserved synteny. The second, a bottom-up approach, predicts novel phenotypes of the species by calculating profiles of each Pfam domain among their genomes and following pair-wise correlation of the profiles and their network clustering. Using the first approach, we find a link between cold and salt tolerance of the species and the presence in the genome of a Na+/H+ antiporter gene cluster. Other cold-tolerance-related genes include peptidases, chemotaxis sensory transducer proteins, a cysteine exporter, and helicases. Using the bottom-up approach, we found several novel phenotypes in the newly sequenced Shewanella species, including degradation of aromatic compounds by an aerobic hybrid pathway in Shewanella woodyi, degradation of ethanolamine by Shewanella benthica, and propanediol degradation by Shewanella putrefaciens CN32 and Shewanella sp. W3-18-1.
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9
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Nahum LA, Goswami S, Serres MH. Protein families reflect the metabolic diversity of organisms and provide support for functional prediction. Physiol Genomics 2009; 38:250-60. [PMID: 19491149 DOI: 10.1152/physiolgenomics.90244.2008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Comparative genomics has shown that protein families vary significantly within and across organisms in both number and functional composition. In the present work, we tested how the diversity at the family level reflects biological differences among organisms and contributes to their unique characteristics. For this purpose, we collected sequence-similar proteins of three selected families from model bacteria: Escherichia coli, Bacillus subtilis, and Pseudomonas aeruginosa. Protein relationships were identified using a phylogenomic approach to connect the functional diversity of enzymes to the metabolic capabilities of these organisms. All protein families studied have distinct functional compositions across the selected bacteria as supported by our Bayesian analysis. Some conserved functional features among family members included a shared reaction mechanism, cofactor usage, and/or ligand specificity. Many observations of the presence/absence of protein functions matched current knowledge of the physiology and biochemistry of the bacteria. In some cases, new functional predictions were made to family members previously uncharacterized. We believe that genome comparisons at the protein family level would also be useful in predicting metabolic diversity for organisms that are relatively unknown or currently uncultured in the laboratory.
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Affiliation(s)
- Laila A Nahum
- The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts
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10
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Fredrickson JK, Romine MF, Beliaev AS, Auchtung JM, Driscoll ME, Gardner TS, Nealson KH, Osterman AL, Pinchuk G, Reed JL, Rodionov DA, Rodrigues JLM, Saffarini DA, Serres MH, Spormann AM, Zhulin IB, Tiedje JM. Towards environmental systems biology of Shewanella. Nat Rev Microbiol 2008; 6:592-603. [PMID: 18604222 DOI: 10.1038/nrmicro1947] [Citation(s) in RCA: 622] [Impact Index Per Article: 38.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Bacteria of the genus Shewanella are known for their versatile electron-accepting capacities, which allow them to couple the decomposition of organic matter to the reduction of the various terminal electron acceptors that they encounter in their stratified environments. Owing to their diverse metabolic capabilities, shewanellae are important for carbon cycling and have considerable potential for the remediation of contaminated environments and use in microbial fuel cells. Systems-level analysis of the model species Shewanella oneidensis MR-1 and other members of this genus has provided new insights into the signal-transduction proteins, regulators, and metabolic and respiratory subsystems that govern the remarkable versatility of the shewanellae.
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Affiliation(s)
- James K Fredrickson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA. ;
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11
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Driscoll ME, Romine MF, Juhn FS, Serres MH, McCue LA, Beliaev AS, Fredrickson JK, Gardner TS. Identification of diverse carbon utilization pathways in Shewanella oneidensis MR-1 via expression profiling. Genome Inform 2007; 18:287-298. [PMID: 18546496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
To identify pathways of carbon utilization in the metal-reducing marine bacterium Shewanella oneidensis MR-1, we assayed the expression of cells grown with various carbon sources using a high-density oligonucleotide Affymetrix microarray. Our expression profiles reveal genes and regulatory mechanisms which govern the sensing, import, and utilization of the nucleoside inosine, the chitin monomer N-acetylglucosamine, and a casein-derived mixture of amino acids. Our analysis suggests a prominent role for the pentose-phosphate and Entner-Doudoroff pathways in energy metabolism, and regulatory coupling between carbon catabolism and electron acceptor pathways. In sum, these results indicate that S. oneidensis possesses a broader capacity for carbon utilization than previously reported, a view with implications for optimizing its role in microbial fuel cell and bioremediative applications.
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Abstract
Genomic sequences have been used to find the genetic foundation for carbon source metabolism in Shewanella oneidensis MR-1. Annotated S. oneidensis MR-1 gene products were examined for their sequence similarity to enzymes participating in pathways for utilization of carbon and energy as described in the BioCyc database (http://www.biocyc.org/) or in the primary literature. A picture emerges that relegates five- and six-carbon sugars to minor roles as carbon sources, whereas multiple pathways for utilization of up to three-carbon carbohydrates seem to be present. Capacity to utilize amino acids for carbon and energy is also present. A few contradictions emerged in which enzymes appear to be present by annotations but are not active in the cell according to physiological experiments. Annotations are based on close sequence similarity and will not reveal inactivity due to deleterious mutations or due to lack of coordination of regulation and transport. Genes for a few enzymes known by experiment to be active are not found in the genome. This may be due to extensive divergence after duplication or convergence of function in separate lines in evolution rendering activities undetectable by sequence similarity. To minimize false predictions from protein sequences, we have been conservative in predicting pathways. We did not predict any pathway when, although a partial pathway was seen it was composed largely of enzymes already accounted for in any other complete pathway. This is an example of how a biochemically oriented sequence analysis can generate questions and direct further experimental investigation.
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Affiliation(s)
- Margrethe H Serres
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA
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13
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Riley M, Abe T, Arnaud MB, Berlyn MKB, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL. Escherichia coli K-12: a cooperatively developed annotation snapshot--2005. Nucleic Acids Res 2006; 34:1-9. [PMID: 16397293 PMCID: PMC1325200 DOI: 10.1093/nar/gkj405] [Citation(s) in RCA: 404] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The goal of this group project has been to coordinate and bring up-to-date information on all genes of Escherichia coli K-12. Annotation of the genome of an organism entails identification of genes, the boundaries of genes in terms of precise start and end sites, and description of the gene products. Known and predicted functions were assigned to each gene product on the basis of experimental evidence or sequence analysis. Since both kinds of evidence are constantly expanding, no annotation is complete at any moment in time. This is a snapshot analysis based on the most recent genome sequences of two E.coli K-12 bacteria. An accurate and up-to-date description of E.coli K-12 genes is of particular importance to the scientific community because experimentally determined properties of its gene products provide fundamental information for annotation of innumerable genes of other organisms. Availability of the complete genome sequence of two K-12 strains allows comparison of their genotypes and mutant status of alleles.
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Affiliation(s)
- Monica Riley
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA.
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14
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Abstract
Background Escherichia coli a model organism provides information for annotation of other genomes. Our analysis of its genome has shown that proteins encoded by fused genes need special attention. Such composite (multimodular) proteins consist of two or more components (modules) encoding distinct functions. Multimodular proteins have been found to complicate both annotation and generation of sequence similar groups. Previous work overstated the number of multimodular proteins in E. coli. This work corrects the identification of modules by including sequence information from proteins in 50 sequenced microbial genomes. Results Multimodular E. coli K-12 proteins were identified from sequence similarities between their component modules and non-fused proteins in 50 genomes and from the literature. We found 109 multimodular proteins in E. coli containing either two or three modules. Most modules had standalone sequence relatives in other genomes. The separated modules together with all the single (un-fused) proteins constitute the sum of all unimodular proteins of E. coli. Pairwise sequence relationships among all E. coli unimodular proteins generated 490 sequence similar, paralogous groups. Groups ranged in size from 92 to 2 members and had varying degrees of relatedness among their members. Some E. coli enzyme groups were compared to homologs in other bacterial genomes. Conclusion The deleterious effects of multimodular proteins on annotation and on the formation of groups of paralogs are emphasized. To improve annotation results, all multimodular proteins in an organism should be detected and when known each function should be connected with its location in the sequence of the protein. When transferring functions by sequence similarity, alignment locations must be noted, particularly when alignments cover only part of the sequences, in order to enable transfer of the correct function. Separating multimodular proteins into module units makes it possible to generate protein groups related by both sequence and function, avoiding mixing of unrelated sequences. Organisms differ in sizes of groups of sequence-related proteins. A sample comparison of orthologs to selected E. coli paralogous groups correlates with known physiological and taxonomic relationships between the organisms.
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Affiliation(s)
- Margrethe H Serres
- Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA02543-1015, USA
| | - Monica Riley
- Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA02543-1015, USA
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15
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Kolker E, Picone AF, Galperin MY, Romine MF, Higdon R, Makarova KS, Kolker N, Anderson GA, Qiu X, Auberry KJ, Babnigg G, Beliaev AS, Edlefsen P, Elias DA, Gorby YA, Holzman T, Klappenbach JA, Konstantinidis KT, Land ML, Lipton MS, McCue LA, Monroe M, Pasa-Tolic L, Pinchuk G, Purvine S, Serres MH, Tsapin S, Zakrajsek BA, Zhu W, Zhou J, Larimer FW, Lawrence CE, Riley M, Collart FR, Yates JR, Smith RD, Giometti CS, Nealson KH, Fredrickson JK, Tiedje JM. Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations. Proc Natl Acad Sci U S A 2005; 102:2099-104. [PMID: 15684069 PMCID: PMC548307 DOI: 10.1073/pnas.0409111102] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.3] [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] [Indexed: 11/18/2022] Open
Abstract
The gamma-proteobacterium Shewanella oneidensis strain MR-1 is a metabolically versatile organism that can reduce a wide range of organic compounds, metal ions, and radionuclides. Similar to most other sequenced organisms, approximately 40% of the predicted ORFs in the S. oneidensis genome were annotated as uncharacterized "hypothetical" genes. We implemented an integrative approach by using experimental and computational analyses to provide more detailed insight into gene function. Global expression profiles were determined for cells after UV irradiation and under aerobic and suboxic growth conditions. Transcriptomic and proteomic analyses confidently identified 538 hypothetical genes as expressed in S. oneidensis cells both as mRNAs and proteins (33% of all predicted hypothetical proteins). Publicly available analysis tools and databases and the expression data were applied to improve the annotation of these genes. The annotation results were scored by using a seven-category schema that ranked both confidence and precision of the functional assignment. We were able to identify homologs for nearly all of these hypothetical proteins (97%), but could confidently assign exact biochemical functions for only 16 proteins (category 1; 3%). Altogether, computational and experimental evidence provided functional assignments or insights for 240 more genes (categories 2-5; 45%). These functional annotations advance our understanding of genes involved in vital cellular processes, including energy conversion, ion transport, secondary metabolism, and signal transduction. We propose that this integrative approach offers a valuable means to undertake the enormous challenge of characterizing the rapidly growing number of hypothetical proteins with each newly sequenced genome.
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Affiliation(s)
- Eugene Kolker
- BIATECH, 19310 North Creek Parkway, Suite 115, Bothell, WA 98011, USA.
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Serres MH, Riley M. Structural Domains, Protein Modules, and Sequence Similarities Enrich Our Understanding of theShewanella oneidensisMR-1 Proteome. OMICS: A Journal of Integrative Biology 2004; 8:306-21. [PMID: 15703478 DOI: 10.1089/omi.2004.8.306] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The protein coding sequences of S. oneidensis MR-1 were analyzed, and new annotations were given to 491 gene products, 306 of which were previously of unknown function. New information was mainly brought in from structural domain predictions for S. oneidensis proteins of the SUPERFAM database (http://supfam.mrc-lmb.cam.ac.uk/SUPERFAMILY/) and newly identified and experimentally verified functions of homologous proteins. Proteins encoded by fused genes were identified and separated into modules, protein units of at least 83 aa with independent functions and distinct evolutionary histories. A reannotation of the fused gene products was done to assign functions to the appropriate module within the protein. Groups of sequence-similar proteins of S. oneidensis were assembled. The fused gene products were represented by their modular entities for the grouping process. The protein groups were analyzed for their size and functions, and they were used to indicate activities that are of importance to the environmental adaptation of this organism. Making use of several approaches not commonly used in annotation, we have been able to enrich our understanding of the functions encoded by the S. oneidensis genome.
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Affiliation(s)
- Margrethe H Serres
- Marine Biological Laboratory, Woods Hole, Massachusetts 02543-1015, USA.
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Abstract
Using more than one approach to characterizing functions of unknown proteins, we now present in GenProtEC (http://genprotec.mbl.edu/) some level of function information for 87% of Escherichia coli K-12 proteins. A new approach that has yielded new information entails assigning content of structural domains and their functions to E.coli proteins. In addition, some earlier methods have been further refined to provide more meaningful data. The process of identifying and separating multimodular or fused proteins into component modules has been improved. As a result, groups of sequence-similar (paralogous) proteins have been refined. Experimental information from recent literature on previously unknown genes has been incorporated. We now use a rich system of characterizing cell roles which accents the fact that many proteins play more than one cellular role and therefore carry more than one designation from our detailed catalog of roles, MultiFun.
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Abstract
An enriched classification system for cellular functions of gene products of Escherichia coli K-12 was developed based on the initial classification by Riley. In the new classification scheme, MultiFun, cellular functions are divided into 10 major categories: Metabolism, Information Transfer, Regulation, Transport, Cell Processes, Cell Structure, Location, Extra-chromosomal Origin, DNA Site, and Cryptic Gene. These major categories are further sub-divided into a hierarchical scheme. Two thousand nine hundred twenty-two gene products of E. coli K-12 were assigned to one or more functions depending on the role they play in the cell. Functional assignments were made to 66% of E. coli gene products, ranging from 1 to 16 assignments per gene product. The expansion of cellular function categories and the assignment to more than one category (multifunction) provides a more complete description of the gene products and their roles and hence better reflects the functional complexity of organisms. We believe this classification system will be useful in the field of genome analysis, both for annotation purposes and for comparative studies. The functional classification scheme and the cellular function assignments made to E. coli gene products can be accessed from the web at the databases GenProtEC (http://genprotec.mbl.edu) and EcoCyc (http://www.ecocyc.org).
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Affiliation(s)
- M H Serres
- The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts 02543, USA
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Abstract
We present a summary of recent progress in understanding Escherichia coli K-12 gene and protein functions. New information has come both from classical biological experimentation and from using the analytical tools of functional genomics. The content of the E. coli genome can clearly be seen to contain elements acquired by horizontal transfer. Nevertheless, there is probably a large, stable core of >3500 genes that are shared among all E. coli strains. The gene-enzyme relationship is examined, and, in many cases, it exhibits complexity beyond a simple one-to-one relationship. Also, the E. coli genome can now be seen to contain many multiple enzymes that carry out the same or closely similar reactions. Some are similar in sequence and may share common ancestry; some are not. We discuss the concept of a minimal genome as being variable among organisms and obligatorily linked to their life styles and defined environmental conditions. We also address classification of functions of gene products and avenues of insight into the history of protein evolution.
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Affiliation(s)
- M Riley
- The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts 02543, USA. ,
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Serres MH, Gopal S, Nahum LA, Liang P, Gaasterland T, Riley M. A functional update of the Escherichia coli K-12 genome. Genome Biol 2001; 2:RESEARCH0035. [PMID: 11574054 PMCID: PMC56896 DOI: 10.1186/gb-2001-2-9-research0035] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2001] [Revised: 06/08/2001] [Accepted: 07/10/2001] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Since the genome of Escherichia coli K-12 was initially annotated in 1997, additional functional information based on biological characterization and functions of sequence-similar proteins has become available. On the basis of this new information, an updated version of the annotated chromosome has been generated. RESULTS The E. coli K-12 chromosome is currently represented by 4,401 genes encoding 116 RNAs and 4,285 proteins. The boundaries of the genes identified in the GenBank Accession U00096 were used. Some protein-coding sequences are compound and encode multimodular proteins. The coding sequences (CDSs) are represented by modules (protein elements of at least 100 amino acids with biological activity and independent evolutionary history). There are 4,616 identified modules in the 4,285 proteins. Of these, 48.9% have been characterized, 29.5% have an imputed function, 2.1% have a phenotype and 19.5% have no function assignment. Only 7% of the modules appear unique to E. coli, and this number is expected to be reduced as more genome data becomes available. The imputed functions were assigned on the basis of manual evaluation of functions predicted by BLAST and DARWIN analyses and by the MAGPIE genome annotation system. CONCLUSIONS Much knowledge has been gained about functions encoded by the E. coli K-12 genome since the 1997 annotation was published. The data presented here should be useful for analysis of E. coli gene products as well as gene products encoded by other genomes.
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Affiliation(s)
- M H Serres
- The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA.
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Abstract
An ultrasensitive assay is described for microcystin-LR and other substances (microcystins, nodularin, okadaic acid, calyculin A, tautomycin) which block the active site of protein phosphatases (PP) 1 and 2A. The assay is based on competition between the unknown sample and [125I]microcystin-YR for binding to the catalytic subunit of PP2A. The PP2A-bound [125I]microcystin-YR was stable (half-time of dissociation = 1.8 h), allowing non-bound [125I]microcystin-YR to be removed by Sephadex G-50 size-exclusion chromatography. Compared to current assays based on inhibition of protein phosphatase activity the present assay was more robust against interference (from fluoride, ATP, histone, and casein), and had an even better sensitivity. The detection limit was below 50 pM (2.5 fmol) for nodularin and microcystin-LR, and below 200 pM (10 fmol) for okadaic acid. The method was used successfully to detect extremely low concentrations of either microcystin or nodularin in drinking water or seawater, and okadaic acid in shellfish extract.
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Affiliation(s)
- M H Serres
- Department of Anatomy and Cell Biology, University of Bergen, Norway
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Fladmark KE, Serres MH, Larsen NL, Yasumoto T, Aune T, Døskeland SO. Sensitive detection of apoptogenic toxins in suspension cultures of rat and salmon hepatocytes. Toxicon 1998; 36:1101-14. [PMID: 9690778 DOI: 10.1016/s0041-0101(98)00083-x] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A number of algal toxins were tested for the ability to induce apoptosis (regulated cell death) in primary hepatocytes from salmon and rat. The tested toxins included the liver targeting substances microcystin-LR and nodularin, substances associated with the diarrhetic shellfish poison complex (okadaic acid, dinophysistoxin-1 and pectenotoxin-1) and calyculin A. All toxins induced apoptosis in both salmon and rat hepatocytes in less than 2 h. The apoptotic changes were evident both by electron and light microscopy and were counteracted by the caspase inhibitor ZVAD-fmk and by the Ca2+/calmodulin dependent kinase II inhibitor KN-93. The salmon hepatocytes were 10-20-fold more sensitive to okadaic acid and dinophysistoxin-1 (EC50=20 nM) than rat hepatocytes and other mammalian cell lines tested. An assay was devised using hepatocyte apoptosis as parameter for detection of algal toxins. This assay was at least as sensitive as HPLC determination for okadaic acid in mussel extracts. It also detected algal toxins which do not inhibit protein phosphatases, like pectenotoxin-1. Subapoptotic concentrations of the toxins inhibited hepatocyte aggregation. Using this parameter, less than 200 pg okadaic acid could be detected. In conclusion, salmon hepatocytes in suspension culture provide a rapid and sensitive system for detection of a broad range of apoptogenic toxins.
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Affiliation(s)
- K E Fladmark
- Cell Biology Research Group, Department of Anatomy and Cell Biology, University of Bergen, Norway
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Abstract
Endogenous ADP-ribosylation of two proteins with molecular weights of 30,000 (30K) and 80,000 (80K) was detected in cell extracts of Mycobacterium smegmatis. Modification of these proteins was enzymatic. The ADP-ribose bound to 30K was removed by HgCl2 but not by NH2OH, suggesting the modification of a cysteine residue. The ADP-ribose bound to 80K was not removed by either HgCl2 or NH2OH, which is consistent with the modification of an asparagine residue. ADP-ribosylation of 80K appeared to be reversible.
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Affiliation(s)
- M H Serres
- Department of Bacteriology, University of Wisconsin--Madison, 53706, USA
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