ARCHIVED - International Community Completes Annotation of the Candida Albicans Genome

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June 04, 2004— Ottawa, Ontario

 

This photo     shows Candida wild-type strains interacting with RAW264.7 mouse macrophage cells (nuclei stained with Hoescht 33342).
This photo shows Candida wild-type strains interacting with RAW264.7 mouse macrophage cells (nuclei stained with Hoescht 33342).

An international effort spearheaded by scientists at the National Research Council Biotechnology Research Institute (NRC-BRI) in Montreal has resulted in the first complete annotation of the Candida albicans genome, a medically important human fungal pathogen. The genome of this potentially fatal fungus had previously been sequenced, at least partially, but never fully annotated. In today's genomic world, a sequenced genome is not completely useful until it has been annotated – a feat made possible only by human intervention.

The annotation process started in 2002 and required approximately two years of work to define the complete collection of protein-coding sequences of the genome. The annotation was presented at a special session of the ASM conference on Candida and Candidiasis in Austin in March 2004.

DNA Microarray Technology

A microarray is an orderly arrangement of DNA samples on a glass slide. A postage stamp-sized array may contain thousands of spots of DNA molecules, each spot representing a particular gene. In contrast to early work that focused on the function of a single gene, an array experiment can look at the entire genome and assess the expression and interactions of all of the genes of an organism simultaneously.

What makes the NRC-BRI MicroArray Lab unique in Canada is the coupling of microarray fabrication with high throughput synthesis of genetic material. They can make a DNA chip from an organism about which there is little current information. The lab also offers assistance in collecting and analyzing the data from a DNA chip experiment.

Candida albicans, a common yet sometimes fatal pathogen, is one of the leading causes of infections affecting immunodeficient individuals. An estimated 30% of severe fungal infections, most due to Candida, result in death. Those who are most at risk include individuals taking immune-suppressive drugs following transplant operations, people with HIV infection and individuals undergoing cancer therapy. Candida, a common natural component of human micro-flora, is found primarily within the human digestive system and mucosal surfaces, but it can cause systemic infections when the immune system is weakened and there is a decrease of healthy bacteria within the body.

Generally speaking, Candida infections are difficult to treat within the at-risk population. Current therapies for this pathogen are ineffective due to drug resistance and significant secondary effects of anti-fungal drugs that target proteins that are also found in the human host.

"Certain courses of action can be taken with impunity when dealing with bacteria, because the treatments won't affect us," explained Dr. Malcolm Whiteway, leader of NRC-BRI's Genetics group. "It's a significantly different situation when it comes to a fungus. Actions taken to kill the fungus will often have an impact on the host as well."

Microarray read-out.
Microarray read-out.

Confronted with this biological hurdle, practitioners must have a comprehensive understanding of this organism in order to target the pathogen's weaker defenses. One key tool in this effort is DNA microarray technology. Based on longstanding expertise in a related organism, Saccharomyces cerevisiae (also known as baker's yeast), the NRC-BRI team managed to produce the first non-commercial Candida arrays for use by the international scientific community. Currently, the institute sells chips containing the Candida microarray to academic and research groups worldwide, and to private companies in Canada.

In order to annotate the Candida genome, Dr. André Nantel, acting project leader of the MicroArray Lab at NRC-BRI, and his colleagues spearheaded an international cooperative effort by uniting the Canadian and international Candida communities.

Sequences already existed but they had not been "put together into the different genes," explains Dr. Whiteway. "It was simply just stretches of A's, T's, C's and G's." Researchers were called upon to systematically verify sections of the genome according to their area of expertise, to see whether computer-generated predictions of the genes were correct.

DNA microarray.
DNA microarray.

The first step in the annotation process involved merging data from preliminary annotations produced independently by several groups including the Galar Fungail Consortium in Europe, the NRC-BRI group, and two independent groups composed of researchers from the University of California in San Francisco (UCSF), Stanford and MIT. Bioinformatic merging of these separate datasets was accomplished by computer scientists from the Institut Pasteur in France and the Sanger Centre in the U.K. Funding secured by Dr. Aaron Mitchell of Columbia University (N.Y.) also made this possible.

Timeline

Jan. 2002:
Formation of the Candida annotation working group during the ASM conference on Candida and Candidiasis in Tampa, Fla.

May 2002:
First meeting of the CAWG in Columbia University (N.Y.)

July 2002:
Release of final assembly of the Candida Genome by Stanford Genome Technology Center.

Aug 2002 – Mar 2003:
Merging and reorganization of primary annotation data. Whole genome blast searches.

April – May 2003:
Preparation of the annotation database at the NRC-BRI.

May 2003 – Nov 2003:
Manual annotation of 6354 genes by 15 volunteer annotators from the NRC and UCSF.

Dec 2003 – Feb 2004:
Quality control phase.

Mar 2004 – present:
Whole genome analysis and preparation of scientific publication. Deadline for submission is 30 June 2004.

The Sanger Center's ARTEMIS annotation tool was used in this project. Novel tools were also developed by NRC-BRI, especially in the areas of information exchange and in the visualization of comparative genomics data. These early efforts gave NRC-BRI a significant level of scientific credibility with members of the Candida research community. The tools were used to make initial predictions, and were then followed up by human review – which would decide which of the computer predictions were correct and which were not.

"This is a highly-human driven annotation of the genome," continued Dr. Whiteway. "In other words, if there's a gene that's defined there, it's not just because a computer has said so... it is something somebody has looked at. The result is a much better prediction of what all the important coding sequences are in Candida."

The international community now has a better and easier interpretation of functional genomics and proteomics data on C. albicans. "This is essentially the dictionary for the Candida language," explains Dr. Nantel. "It will directly affect every researcher that works on Candida and fungal pathogenesis."

Typical of annotation efforts – it is a continually evolving process. Researchers want to know – in a given condition or state – which genes are on and which are off – in effect – what regulatory rules are in force at that time. This information is critical in understanding the behaviour of Candida and in finding weaknesses that can be exploited on the way to a treatment or cure.


Enquiries: Media relations
National Research Council of Canada
613-991-1431
media@nrc-cnrc.gc.ca

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