This is a preprint, a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Research Article
Yan Zhang
College of Life Sciences and Oceanography, Shenzhen University
Corresponding Author
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background: Biological trace elements are used in small amounts but are required for all living organisms. They are key components of many proteins and enzymes involved in important biological processes. Many trace element-dependent proteins have been characterized in various microbes, but very little is known about their occurrence, functions, and interactions in microbial communities in marine environments, especially in depth-related marine ecosystems.
Results: In this study, by analyzing metagenomic data from different geographic locations and water depths in the oceans around the world, we identified the distribution of genes encoding trace element-dependent proteins (for copper, molybdenum, tungsten, cobalt, nickel, and selenium) in a variety of marine samples from the upper ocean to the deep sea, which demonstrates vertical patterns of trace element utilization in marine microbes. More than 63,000 metalloprotein and selenoprotein genes belonging to nearly 100 families were predicted, constituting the largest environmental metalloprotein and selenoprotein gene dataset reported so far. Further examination of the interactions among trace elements revealed significant correlations between some of them (especially molybdenum or tungsten and selenium) and more active elemental crosstalk in the epipelagic zone of the ocean. Comparison of the patterns of trace element utilization across samples suggested that additional unknown factors might play a more important role in shaping trace element utilization in marine microbes living in certain locations. Finally, analysis of the relationship between water depth and metalloprotein/selenoprotein families revealed that the evolution of approximately half of the metalloprotein and selenoprotein families in marine microbial world could be influenced by ocean depth at either the global or the local level.
Conclusions: Our findings provide new insights into the utilization and functions of trace elements in marine microbes along a vertical gradient across the ocean.
Keywords
Trace element, Marine metagenome, Metalloprotein, Selenoprotein, Depth, Evolution
Figure 1
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Figure 4
This is a list of supplementary files associated with this preprint. Click to download.
- Supplementarytables.xlsx
Additional file 1: Supplementary_tables.xlsx This file contains nine supplementary tables: Table S1 shows all marine metagenomic samples and related information. Table S2 shows the distribution of cuproprotein genes in metagenomic samples. Table S3 shows the distribution of molybdoprotein genes in metagenomic samples. Table S4 shows the distribution of tungstoprotein genes in metagenomic samples. Table S5 shows the distribution of Ni-dependent protein genes in metagenomic samples. Table S6 shows the distribution of Co-dependent protein genes in metagenomic samples. Table S7 shows the distribution of selenoprotein genes in metagenomic samples. Table S8 shows the assembly statistics for metagenomic samples. Table S9 shows the list of known metalloproteins (Cu, Mo, W, Ni, and Co) and selenoproteins in prokaryotes.
- Supplementaryfigures.pdf
Additional file 2: Supplementary_figures.pdf This file contains eight supplementary figures: Figure S1 shows geographic locations of marine metagenomic samples. Figure S2 shows the distribution of cuproproteomes in marine metagenomic samples. Figure S3 shows the distribution of molybdoproteomes in marine metagenomic samples. Figure S4 shows the distribution of tungstoproteomes in marine metagenomic samples. Figure S5 shows the distribution of Ni-dependent proteomes in marine metagenomic samples. Figure S6 shows the distribution of Co-dependent proteomes in marine metagenomic samples. Figure S7 shows putative taxonomic affiliation of RNR II sequences detected in the metagenomic dataset. Figure S8 shows the distribution of selenoproteomes in marine metagenomic samples.
- sequencedataset.txt
Additional file 3: sequence_dataset.txt This file contains all metalloprotein and selenoprotein sequences analyzed in this study.
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This is a preprint, a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Research Article
Yan Zhang
College of Life Sciences and Oceanography, Shenzhen University
Corresponding Author
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
History
CURRENT STATUS: Posted
Version 1
Posted 12 Jan, 2021
No community comments so far
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Epigenetics & Genomics
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background: Biological trace elements are used in small amounts but are required for all living organisms. They are key components of many proteins and enzymes involved in important biological processes. Many trace element-dependent proteins have been characterized in various microbes, but very little is known about their occurrence, functions, and interactions in microbial communities in marine environments, especially in depth-related marine ecosystems.
Results: In this study, by analyzing metagenomic data from different geographic locations and water depths in the oceans around the world, we identified the distribution of genes encoding trace element-dependent proteins (for copper, molybdenum, tungsten, cobalt, nickel, and selenium) in a variety of marine samples from the upper ocean to the deep sea, which demonstrates vertical patterns of trace element utilization in marine microbes. More than 63,000 metalloprotein and selenoprotein genes belonging to nearly 100 families were predicted, constituting the largest environmental metalloprotein and selenoprotein gene dataset reported so far. Further examination of the interactions among trace elements revealed significant correlations between some of them (especially molybdenum or tungsten and selenium) and more active elemental crosstalk in the epipelagic zone of the ocean. Comparison of the patterns of trace element utilization across samples suggested that additional unknown factors might play a more important role in shaping trace element utilization in marine microbes living in certain locations. Finally, analysis of the relationship between water depth and metalloprotein/selenoprotein families revealed that the evolution of approximately half of the metalloprotein and selenoprotein families in marine microbial world could be influenced by ocean depth at either the global or the local level.
Conclusions: Our findings provide new insights into the utilization and functions of trace elements in marine microbes along a vertical gradient across the ocean.
Figure 1
Figure 2
Figure 3
Figure 4
This is a list of supplementary files associated with this preprint. Click to download.
- Supplementarytables.xlsx
Additional file 1: Supplementary_tables.xlsx This file contains nine supplementary tables: Table S1 shows all marine metagenomic samples and related information. Table S2 shows the distribution of cuproprotein genes in metagenomic samples. Table S3 shows the distribution of molybdoprotein genes in metagenomic samples. Table S4 shows the distribution of tungstoprotein genes in metagenomic samples. Table S5 shows the distribution of Ni-dependent protein genes in metagenomic samples. Table S6 shows the distribution of Co-dependent protein genes in metagenomic samples. Table S7 shows the distribution of selenoprotein genes in metagenomic samples. Table S8 shows the assembly statistics for metagenomic samples. Table S9 shows the list of known metalloproteins (Cu, Mo, W, Ni, and Co) and selenoproteins in prokaryotes.
- Supplementaryfigures.pdf
Additional file 2: Supplementary_figures.pdf This file contains eight supplementary figures: Figure S1 shows geographic locations of marine metagenomic samples. Figure S2 shows the distribution of cuproproteomes in marine metagenomic samples. Figure S3 shows the distribution of molybdoproteomes in marine metagenomic samples. Figure S4 shows the distribution of tungstoproteomes in marine metagenomic samples. Figure S5 shows the distribution of Ni-dependent proteomes in marine metagenomic samples. Figure S6 shows the distribution of Co-dependent proteomes in marine metagenomic samples. Figure S7 shows putative taxonomic affiliation of RNR II sequences detected in the metagenomic dataset. Figure S8 shows the distribution of selenoproteomes in marine metagenomic samples.
- sequencedataset.txt
Additional file 3: sequence_dataset.txt This file contains all metalloprotein and selenoprotein sequences analyzed in this study.
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