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Title: Genome-Facilitated Analyses of Geomicrobial Processes

Abstract

This project had the goal(s) of understanding the mechanism(s) of extracellular electron transport (EET) in the microbe Shewanella oneidensis MR-1, and a number of other strains and species in the genus Shewanella. The major accomplishments included sequencing, annotation, and analysis of more than 20 Shewanella genomes. The comparative genomics enabled the beginning of a systems biology approach to this genus. Another major contribution involved the study of gene regulation, primarily in the model organism, MR-1. As part of this work, we took advantage of special facilities at the DOE: e.g., the synchrotron radiation facility at ANL, where we successfully used this system for elemental characterization of single cells in different metabolic states (1). We began work with purified enzymes, and identification of partially purified enzymes, leading to initial characterization of several of the 42 c-type cytochromes from MR-1 (2). As the genome became annotated, we began experiments on transcriptome analysis under different conditions of growth, the first step towards systems biology (3,4). Conductive appendages of Shewanella, called bacterial nanowires were identified and characterized during this work (5, 11, 20,21). For the first time, it was possible to measure the electron transfer rate between single cells and a solid substrate (20),more » a rate that has been confirmed by several other laboratories. We also showed that MR-1 cells preferentially attach to cells at a given charge, and are not attracted, or even repelled by other charges. The interaction with the charged surfaces begins with a stimulation of motility (called electrokinesis), and eventually leads to attachment and growth. One of the things that genomics allows is the comparative analysis of the various Shewanella strains, which led to several important insights. First, while the genomes predicted that none of the strains looked like they should be able to degrade N-acetyl glucosamine (NAG), the monomer that makes up chitin, virtually all of the strains were in fact capable. This led to the discovery of a great many new genes involved with chitin and NAG metabolism (7). In a similar vein, a detailed study of the sugar utilization pathway revealed a major new insight into the regulation of sugar metabolism in this genus (19). Systems Biology and Comparative Genomics of the shewanellae: Several publications were put together describing the use of comparative genomics for analyses of the group Shewanella, and these were a logical culmination of our genomic-driven research (10,15,18). Eight graduate students received their Ph.D. degrees doing part of the work described here, and four postdoctoral fellows were supported. In addition, approximately 20 undergraduates took part in projects during the grant period.« less

Authors:
Publication Date:
Research Org.:
Univ. of Southern California, Los Angeles, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1039338
Report Number(s):
DOE/ER/63882-Final Report
TRN: US201214%%1001
DOE Contract Number:  
FG02-04ER63882
Resource Type:
Technical Report
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 54 ENVIRONMENTAL SCIENCES; 58 GEOSCIENCES; ANL; BIOLOGY; CHITIN; CYTOCHROMES; ELECTRON TRANSFER; ELECTRONS; ENZYMES; GENE REGULATION; GENES; GLUCOSAMINE; METABOLISM; MONOMERS; REGULATIONS; SACCHAROSE; STIMULATION; STRAINS; SUBSTRATES; SYNCHROTRON RADIATION; Shewanella, electron transport, environmental microbiology, metal reduction, microbial genomics

Citation Formats

Nealson, Kenneth H. Genome-Facilitated Analyses of Geomicrobial Processes. United States: N. p., 2012. Web. doi:10.2172/1039338.
Nealson, Kenneth H. Genome-Facilitated Analyses of Geomicrobial Processes. United States. https://doi.org/10.2172/1039338
Nealson, Kenneth H. Wed . "Genome-Facilitated Analyses of Geomicrobial Processes". United States. https://doi.org/10.2172/1039338. https://www.osti.gov/servlets/purl/1039338.
@article{osti_1039338,
title = {Genome-Facilitated Analyses of Geomicrobial Processes},
author = {Nealson, Kenneth H},
abstractNote = {This project had the goal(s) of understanding the mechanism(s) of extracellular electron transport (EET) in the microbe Shewanella oneidensis MR-1, and a number of other strains and species in the genus Shewanella. The major accomplishments included sequencing, annotation, and analysis of more than 20 Shewanella genomes. The comparative genomics enabled the beginning of a systems biology approach to this genus. Another major contribution involved the study of gene regulation, primarily in the model organism, MR-1. As part of this work, we took advantage of special facilities at the DOE: e.g., the synchrotron radiation facility at ANL, where we successfully used this system for elemental characterization of single cells in different metabolic states (1). We began work with purified enzymes, and identification of partially purified enzymes, leading to initial characterization of several of the 42 c-type cytochromes from MR-1 (2). As the genome became annotated, we began experiments on transcriptome analysis under different conditions of growth, the first step towards systems biology (3,4). Conductive appendages of Shewanella, called bacterial nanowires were identified and characterized during this work (5, 11, 20,21). For the first time, it was possible to measure the electron transfer rate between single cells and a solid substrate (20), a rate that has been confirmed by several other laboratories. We also showed that MR-1 cells preferentially attach to cells at a given charge, and are not attracted, or even repelled by other charges. The interaction with the charged surfaces begins with a stimulation of motility (called electrokinesis), and eventually leads to attachment and growth. One of the things that genomics allows is the comparative analysis of the various Shewanella strains, which led to several important insights. First, while the genomes predicted that none of the strains looked like they should be able to degrade N-acetyl glucosamine (NAG), the monomer that makes up chitin, virtually all of the strains were in fact capable. This led to the discovery of a great many new genes involved with chitin and NAG metabolism (7). In a similar vein, a detailed study of the sugar utilization pathway revealed a major new insight into the regulation of sugar metabolism in this genus (19). Systems Biology and Comparative Genomics of the shewanellae: Several publications were put together describing the use of comparative genomics for analyses of the group Shewanella, and these were a logical culmination of our genomic-driven research (10,15,18). Eight graduate students received their Ph.D. degrees doing part of the work described here, and four postdoctoral fellows were supported. In addition, approximately 20 undergraduates took part in projects during the grant period.},
doi = {10.2172/1039338},
url = {https://www.osti.gov/biblio/1039338}, journal = {},
number = ,
volume = ,
place = {United States},
year = {2012},
month = {5}
}