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Related Concept Videos

Environmental Applications of Microorganisms01:30

Environmental Applications of Microorganisms

Microorganisms play a pivotal role in maintaining ecosystem balance by recycling essential elements such as carbon, nitrogen, and phosphorus, as well as supporting processes like bioremediation, wastewater treatment, and biofuel production.Microbes in Elemental CyclesIn the carbon cycle, microorganisms decompose organic matter, releasing carbon dioxide via aerobic respiration. This carbon dioxide is subsequently used by photosynthetic organisms to synthesize organic compounds, closing the...
Deep Sea Microbial Ecology01:18

Deep Sea Microbial Ecology

The deep ocean and its underlying sediments represent vast, largely unexplored microbial habitats that extend far beyond the sunlit photic zone. The photic (euphotic) zone typically spans the upper ~100–200 meters of pelagic waters in the open ocean, but its depth varies geographically and seasonally, where sufficient light supports photosynthetic life. Below this lies the deep sea, spanning roughly 1000–6000 meters (bathypelagic to abyssal zones), with deeper hadal trenches extending beyond...
Proteomics01:33

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
Evolution of Microbial Genome01:08

Evolution of Microbial Genome

Microbial genome evolution is a highly dynamic process shaped by continual gene gain and loss across species and strains. This genomic flexibility allows microorganisms to adapt rapidly to environmental pressures and interactions with other organisms. Central to understanding this diversity is the distinction between the core and pan genomes.The core genome comprises the genes shared by all sampled strains of a species, representing essential functions needed for fundamental cellular processes.
Microbial Biosensors01:17

Microbial Biosensors

Microbial biosensors are analytical devices that utilize living microbes to detect specific substances through measurable signals. These devices consist of two main components: biosensing organisms and signal-transducing elements. Biosensing organisms, such as Escherichia coli or Saccharomyces cerevisiae, are typically housed in multiwell plates connected to transducers, enabling rapid, real-time detection of target analytes.Signal Generation MechanismWhen a target analyte—such as...

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Related Experiment Video

Updated: May 11, 2026

An Aquatic Microbial Metaproteomics Workflow: From Cells to Tryptic Peptides Suitable for Tandem Mass Spectrometry-based Analysis
08:09

An Aquatic Microbial Metaproteomics Workflow: From Cells to Tryptic Peptides Suitable for Tandem Mass Spectrometry-based Analysis

Published on: September 15, 2015

Proteogenomics for environmental microbiology.

Jean Armengaud1, Erica Marie Hartmann, Céline Bland

  • 1CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze, France.

Proteomics
|May 3, 2013
PubMed
Summary

Proteogenomics integrates genomic and proteomic data to improve genome annotation, especially for microorganisms. This approach refines gene structures and functions, advancing environmental microbiology research.

Keywords:
Genome annotationHigh-throughput proteomicsMicrobiologyN-TerminomicsProteogenomicsTranslational start site

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Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons

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Related Experiment Videos

Last Updated: May 11, 2026

An Aquatic Microbial Metaproteomics Workflow: From Cells to Tryptic Peptides Suitable for Tandem Mass Spectrometry-based Analysis
08:09

An Aquatic Microbial Metaproteomics Workflow: From Cells to Tryptic Peptides Suitable for Tandem Mass Spectrometry-based Analysis

Published on: September 15, 2015

Analyzing Gene Expression from Marine Microbial Communities using Environmental Transcriptomics
13:51

Analyzing Gene Expression from Marine Microbial Communities using Environmental Transcriptomics

Published on: February 18, 2009

Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons
10:24

Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons

Published on: August 29, 2014

Area of Science:

  • Genomics and Proteomics
  • Environmental Microbiology

Background:

  • Automatic genome annotation pipelines have limitations, leading to errors in gene structure and functional assignment.
  • Challenges in annotating poorly documented microbial genera and identifying short or orphan genes are significant.
  • High-throughput shotgun proteomics offers deep exploration of microbial proteomes, complementing genomic data.

Purpose of the Study:

  • To highlight the utility of proteogenomics in refining genome annotation.
  • To demonstrate how integrating proteomic data addresses limitations in genomic annotation.
  • To showcase advancements in N-terminomics for validating translational start codons and secreted proteins.

Main Methods:

  • Proteogenomic mapping using experimental proteomic data.
  • N-terminomics for systematic identification of protein N-termini.
  • High-throughput shotgun proteomics for deep proteome exploration.
  • Combined bottom-up and top-down proteomic approaches.

Main Results:

  • Proteogenomic mapping has been successfully applied across diverse organisms.
  • N-terminomics provides experimentally validated translational start codons and signals for secreted proteins.
  • Integration of genomic and proteomic data is becoming standard practice in research.

Conclusions:

  • Proteogenomics enhances the accuracy of genome structural and functional annotation.
  • The integration of proteomics and genomics is crucial for advancing environmental microbiology.
  • New proteogenomic strategies are essential for understanding microbial life.