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Structural genomics studies of human caries pathogen Streptococcus mutans

Li, Lanfen; Nan, Jie LU ; Li, Dan; Brostromer, Erik; Wang, Zixi; Liu, Cong; Hou, Qiaoming; Fan, Xuexin; Ye, Zhaoyang and Su, Xiao-Dong LU (2014) In Journal of Structural and Functional Genomics 15(3). p.9-91
Abstract

Gram-positive bacterium Streptococcus mutans is the primary causative agent of human dental caries. To better understand this pathogen at the atomic structure level and to establish potential drug and vaccine targets, we have carried out structural genomics research since 2005. To achieve the goal, we have developed various in-house automation systems including novel high-throughput crystallization equipment and methods, based on which a large-scale, high-efficiency and low-cost platform has been establish in our laboratory. From a total of 1,963 annotated open reading frames, 1,391 non-membrane targets were selected prioritized by protein sequence similarities to unknown structures, and clustered by restriction sites to allow for... (More)

Gram-positive bacterium Streptococcus mutans is the primary causative agent of human dental caries. To better understand this pathogen at the atomic structure level and to establish potential drug and vaccine targets, we have carried out structural genomics research since 2005. To achieve the goal, we have developed various in-house automation systems including novel high-throughput crystallization equipment and methods, based on which a large-scale, high-efficiency and low-cost platform has been establish in our laboratory. From a total of 1,963 annotated open reading frames, 1,391 non-membrane targets were selected prioritized by protein sequence similarities to unknown structures, and clustered by restriction sites to allow for cost-effective high-throughput conventional cloning. Selected proteins were over-expressed in different strains of Escherichia coli. Clones expressed soluble proteins were selected, expanded, and expressed proteins were purified and subjected to crystallization trials. Finally, protein crystals were subjected to X-ray analysis and structures were determined by crystallographic methods. Using the previously established procedures, we have so far obtained more than 200 kinds of protein crystals and 100 kinds of crystal structures involved in different biological pathways. In this paper we demonstrate and review a possibility of performing structural genomics studies at moderate laboratory scale. Furthermore, the techniques and methods developed in our study can be widely applied to conventional structural biology research practice.

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author
organization
publishing date
type
Contribution to journal
publication status
published
keywords
Bacterial Proteins, Cloning, Molecular, Computational Biology, Crystallization, Crystallography, X-Ray, Dental Caries, Genome, Bacterial, Genomics, Humans, Image Interpretation, Computer-Assisted, Proteomics, Streptococcus mutans
in
Journal of Structural and Functional Genomics
volume
15
issue
3
pages
9 pages
publisher
Springer Netherlands
external identifiers
  • scopus:84927685880
ISSN
1345-711X
DOI
10.1007/s10969-014-9172-3
language
English
LU publication?
yes
id
981bedcd-0602-4dcb-876f-de967a8de046
date added to LUP
2016-09-07 22:50:23
date last changed
2017-01-01 08:33:30
@article{981bedcd-0602-4dcb-876f-de967a8de046,
  abstract     = {<p>Gram-positive bacterium Streptococcus mutans is the primary causative agent of human dental caries. To better understand this pathogen at the atomic structure level and to establish potential drug and vaccine targets, we have carried out structural genomics research since 2005. To achieve the goal, we have developed various in-house automation systems including novel high-throughput crystallization equipment and methods, based on which a large-scale, high-efficiency and low-cost platform has been establish in our laboratory. From a total of 1,963 annotated open reading frames, 1,391 non-membrane targets were selected prioritized by protein sequence similarities to unknown structures, and clustered by restriction sites to allow for cost-effective high-throughput conventional cloning. Selected proteins were over-expressed in different strains of Escherichia coli. Clones expressed soluble proteins were selected, expanded, and expressed proteins were purified and subjected to crystallization trials. Finally, protein crystals were subjected to X-ray analysis and structures were determined by crystallographic methods. Using the previously established procedures, we have so far obtained more than 200 kinds of protein crystals and 100 kinds of crystal structures involved in different biological pathways. In this paper we demonstrate and review a possibility of performing structural genomics studies at moderate laboratory scale. Furthermore, the techniques and methods developed in our study can be widely applied to conventional structural biology research practice.</p>},
  author       = {Li, Lanfen and Nan, Jie and Li, Dan and Brostromer, Erik and Wang, Zixi and Liu, Cong and Hou, Qiaoming and Fan, Xuexin and Ye, Zhaoyang and Su, Xiao-Dong},
  issn         = {1345-711X},
  keyword      = {Bacterial Proteins,Cloning, Molecular,Computational Biology,Crystallization,Crystallography, X-Ray,Dental Caries,Genome, Bacterial,Genomics,Humans,Image Interpretation, Computer-Assisted,Proteomics,Streptococcus mutans},
  language     = {eng},
  number       = {3},
  pages        = {9--91},
  publisher    = {Springer Netherlands},
  series       = {Journal of Structural and Functional Genomics},
  title        = {Structural genomics studies of human caries pathogen Streptococcus mutans},
  url          = {http://dx.doi.org/10.1007/s10969-014-9172-3},
  volume       = {15},
  year         = {2014},
}