A Global Analysis of Protein Expression Profiles in Sinorhizobium meliloti: Discovery of New Genes for Nodule Occupancy and Stress Adaptation
A proteomic examination of Sinorhizobium meliloti strain 1021 was undertaken using a combination of 2-D gel electrophoresis, peptide mass fingerprinting, and bioinformatics. Our goal was to identify (i) putative symbiosis- or nutrientstress-specific proteins, (ii) the biochemical pathways active und...
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| Format: | Article |
| Language: | English |
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The American Phytopathological Society
2003-06-01
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| Series: | Molecular Plant-Microbe Interactions |
| Subjects: | |
| Online Access: | https://apsjournals.apsnet.org/doi/10.1094/MPMI.2003.16.6.508 |
| _version_ | 1831672356653760512 |
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| author | Michael A. Djordjevic Han Cai Chen Siria Natera Giel Van Noorden Christian Menzel Scott Taylor Clotilde Renard Otto Geiger Georg F. Weiller |
| author_facet | Michael A. Djordjevic Han Cai Chen Siria Natera Giel Van Noorden Christian Menzel Scott Taylor Clotilde Renard Otto Geiger Georg F. Weiller |
| author_sort | Michael A. Djordjevic |
| collection | DOAJ |
| description | A proteomic examination of Sinorhizobium meliloti strain 1021 was undertaken using a combination of 2-D gel electrophoresis, peptide mass fingerprinting, and bioinformatics. Our goal was to identify (i) putative symbiosis- or nutrientstress-specific proteins, (ii) the biochemical pathways active under different conditions, (iii) potential new genes, and (iv) the extent of posttranslational modifications of S. meliloti proteins. In total, we identified the protein products of 810 genes (13.1% of the genome's coding capacity). The 810 genes generated 1,180 gene products, with chromosomal genes accounting for 78% of the gene products identified (18.8% of the chromosome's coding capacity). The activity of 53 metabolic pathways was inferred from bioinformatic analysis of proteins with assigned Enzyme Commission numbers. Of the remaining proteins that did not encode enzymes, ABC-type transporters composed 12.7% and regulatory proteins 3.4% of the total. Proteins with up to seven transmembrane domains were identified in membrane preparations. A total of 27 putative nodulespecific proteins and 35 nutrient-stress-specific proteins were identified and used as a basis to define genes and describe processes occurring in S. meliloti cells in nodules and under stress. Several nodule proteins from the plant host were present in the nodule bacteria preparations. We also identified seven potentially novel proteins not predicted from the DNA sequence. Post-translational modifications such as N-terminal processing could be inferred from the data. The posttranslational addition of UMP to the key regulator of nitrogen metabolism, PII, was demonstrated. This work demonstrates the utility of combining mass spectrometry with protein arraying or separation techniques to identify candidate genes involved in important biological processes and niche occupations that may be intransigent to other methods of gene expression profiling. |
| first_indexed | 2024-12-19T23:51:28Z |
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| id | doaj.art-a9f1e27b171e4106aea8801646066666 |
| institution | Directory Open Access Journal |
| issn | 0894-0282 1943-7706 |
| language | English |
| last_indexed | 2024-12-19T23:51:28Z |
| publishDate | 2003-06-01 |
| publisher | The American Phytopathological Society |
| record_format | Article |
| series | Molecular Plant-Microbe Interactions |
| spelling | doaj.art-a9f1e27b171e4106aea88016460666662022-12-21T20:01:07ZengThe American Phytopathological SocietyMolecular Plant-Microbe Interactions0894-02821943-77062003-06-0116650852410.1094/MPMI.2003.16.6.508A Global Analysis of Protein Expression Profiles in Sinorhizobium meliloti: Discovery of New Genes for Nodule Occupancy and Stress AdaptationMichael A. DjordjevicHan Cai ChenSiria NateraGiel Van NoordenChristian MenzelScott TaylorClotilde RenardOtto GeigerGeorg F. WeillerA proteomic examination of Sinorhizobium meliloti strain 1021 was undertaken using a combination of 2-D gel electrophoresis, peptide mass fingerprinting, and bioinformatics. Our goal was to identify (i) putative symbiosis- or nutrientstress-specific proteins, (ii) the biochemical pathways active under different conditions, (iii) potential new genes, and (iv) the extent of posttranslational modifications of S. meliloti proteins. In total, we identified the protein products of 810 genes (13.1% of the genome's coding capacity). The 810 genes generated 1,180 gene products, with chromosomal genes accounting for 78% of the gene products identified (18.8% of the chromosome's coding capacity). The activity of 53 metabolic pathways was inferred from bioinformatic analysis of proteins with assigned Enzyme Commission numbers. Of the remaining proteins that did not encode enzymes, ABC-type transporters composed 12.7% and regulatory proteins 3.4% of the total. Proteins with up to seven transmembrane domains were identified in membrane preparations. A total of 27 putative nodulespecific proteins and 35 nutrient-stress-specific proteins were identified and used as a basis to define genes and describe processes occurring in S. meliloti cells in nodules and under stress. Several nodule proteins from the plant host were present in the nodule bacteria preparations. We also identified seven potentially novel proteins not predicted from the DNA sequence. Post-translational modifications such as N-terminal processing could be inferred from the data. The posttranslational addition of UMP to the key regulator of nitrogen metabolism, PII, was demonstrated. This work demonstrates the utility of combining mass spectrometry with protein arraying or separation techniques to identify candidate genes involved in important biological processes and niche occupations that may be intransigent to other methods of gene expression profiling.https://apsjournals.apsnet.org/doi/10.1094/MPMI.2003.16.6.508iron sequesteringMALDI-TOF mass spectrometrymolecular networksNex18reactive oxygen speciesTspO |
| spellingShingle | Michael A. Djordjevic Han Cai Chen Siria Natera Giel Van Noorden Christian Menzel Scott Taylor Clotilde Renard Otto Geiger Georg F. Weiller A Global Analysis of Protein Expression Profiles in Sinorhizobium meliloti: Discovery of New Genes for Nodule Occupancy and Stress Adaptation Molecular Plant-Microbe Interactions iron sequestering MALDI-TOF mass spectrometry molecular networks Nex18 reactive oxygen species TspO |
| title | A Global Analysis of Protein Expression Profiles in Sinorhizobium meliloti: Discovery of New Genes for Nodule Occupancy and Stress Adaptation |
| title_full | A Global Analysis of Protein Expression Profiles in Sinorhizobium meliloti: Discovery of New Genes for Nodule Occupancy and Stress Adaptation |
| title_fullStr | A Global Analysis of Protein Expression Profiles in Sinorhizobium meliloti: Discovery of New Genes for Nodule Occupancy and Stress Adaptation |
| title_full_unstemmed | A Global Analysis of Protein Expression Profiles in Sinorhizobium meliloti: Discovery of New Genes for Nodule Occupancy and Stress Adaptation |
| title_short | A Global Analysis of Protein Expression Profiles in Sinorhizobium meliloti: Discovery of New Genes for Nodule Occupancy and Stress Adaptation |
| title_sort | global analysis of protein expression profiles in sinorhizobium meliloti discovery of new genes for nodule occupancy and stress adaptation |
| topic | iron sequestering MALDI-TOF mass spectrometry molecular networks Nex18 reactive oxygen species TspO |
| url | https://apsjournals.apsnet.org/doi/10.1094/MPMI.2003.16.6.508 |
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