The usual approach to finding out the function of a particular gene in a bacterium, is to somehow inactivate that gene using laboratory procedures and then to observe what are the functional effects. Chlamydiae are almost unique among the important disease-causing bacteria in that there are no methods to directly manipulate their genome. This has forced chlamydiologists to try and derive information about the likely function of a gene by comparison with possible homologues of that gene in other organisms. The approach (genome sequencing) is to determine the identity and order of the nucleotide bases that make up the whole genetic material of chlamydiae. For chlamydiae, these data are published as they become available on the various chlamydial genome sequence web sites [see: links].  Chlamydial genome data may then be compared with similar data for other bacteria where, hopefully, the gene function is already established. Essentially one is looking for homologies of nucleotide sequence of an unknown gene with genes of known function in other, better understood, bacteria. This new science of comparative genomics is facilitated by the availability of international databases of gene and genome sequences, such as GenEMBL, which are readily made available by sites such as the European Bioinformatics Institute or its US equivalent the National Center for Biotechnology Information, for interrogation and comparisons via the web. [The multi find search engine available on the home page of this professional site to persons who have registered and logged in, permits direct searches of chlamydial nucleic acid and protein data].

Normally the genetic code is transcribed via a messenger molecule (messenger or mRNA) [a transcript ] into protein. The order of the amino acids making up a protein is determined by the sequence of nucleotides on the gene, which is read in groups of threes [the genetic code ]. However, the fact that a particular gene is present does not necessarily mean that it is transcribed and translated into protein. The even newer science of proteomics addresses this question and there is a corresponding general web site published by the Swiss Bioinformatics Institute, the Expert Protein Analysis System, Expasy for proteomics. There is also a specialist chlamydial proteomics web site at Aarhus University in Denmark. 

Proteins are complex molecules and their three dimensional structure in space is critical for their function. Three dimensional structure is determined by physical techniques such as X-Ray crystallography or Nuclear Magnetic Resonance (NMR) spectrometry. The data are available via the web from the Protein Data Bank. So far there are no data for the 3-D structure of any chlamydial proteins. 

Here,  the space devoted to chlamydial genomics and proteomics is deliberately brief because of the availability of several good, specialised, chlamydial genome web sites [see: links].

[MEW] May 2002

NEXT: Comparative genomics

INDEX: Biology index