Categories of all C.L. asiaticus proteins

The proteins of Candidatus Liberibacter asiaticus collected in the websites are classified into several categories after automatic prediction and manual curation. Clicking the links will lead to individual list of proteins in the category.

Key Proteins Involved in Metabolic, Genetic and Cellular Process

These proteins are well characterized and conserved in most bacteria and they participate in fundamental processes. Proteins in this category can be further divided into the following sub categories:
Proteins involved in metabolic pathways: most of these proteins are enzymes that catalyze chemical metabolic reactions occurring within the bacterium.In collaboration with Dr. Andrei Osterman, we are trying to build the metabolic network model of C. L. asiaticus with these proteins. Which will provide more evidence to support the function predictions of these proteins and generate a list of essential proteins. Among these essential proteins we will determine potential drug target if certain essential proteins lack orthlogs in the plant or their sequence and structure properties are different enough to allow specific interaction between drug and the bacterium protein.
Proteins for genetic information processing, i.e. proteins that participate DNA replication, DNA repair, transcription and translation.
Proteins needed for cellular process, i.e. proteins participate in transporting, signal transduction, cell movement and division.

Possible Virulence Factors

As a pathogen, this bacteria should secret some virulence factors to interact with the host defence systems and these proteins are essential targets for controlling the disease. It is not a trivial task to identify such proteins. The fact that C.L. asiaticus does not have Type III and Type IV protein secretion system makes it even harder to predict potential effectors, as most effectors identified in other bacteria are secreted by these two secretion system. However, as we manually checked all the proteins in C. L. asiaticus, we are able to get the most suspecious effectors by considering local features, evolutionary history and possible function of the protein deduced from homologs. We are still trying to add more proteins to the list by checking the homology relationship between C. L. asiaticus proteins and known virulence factors from other bacteria.

Phage Proteins

The C. L. asiaticus genome carries integrated prophage, which is confirmed by the recent sequencing of SC1 phage genome [1]. Apart from the entire SC1 prophage genome, this bacteria also prossess other phage proteins, possibly resulting from some ancient integration of phage genome.

Possible Proteins Missed By NCBI Gene Prediction Pipeline

The NCBI gene prediction pipeline missed some possible proteins in the genome, but these proteins were identified by another set of gene prediction pipeline from SEED [2]. Some of these proteins appear to be pseudogenes as stop codons have seperated the genes into two or several pieces. It is possible that some of these genes really have lost their function and become psuedogenes; however, we suspect at least some of them, as they appear to be essential for the survival of the bacteria, should be still expressed as real proteins. Thus we updated our websites and included these proteins to get a more complete view of the bacterium.

Hypothetical Proteins That May Not Be Real

Some proteins, although detected by gene prediction pipelines, barely shows sign of being a real functional protein, since they are too short (less than 50 aa) and not present in other species. We listed all these proteins as well.

[1] Zhang S, Flores-Cruz Z, Zhou L, Kang BH, Fleites LA, Gooch MD, Wulff NA, Davis MJ, Duan YP, Gabriel DW. (2011) Ca. Liberibacter asiaticus' carries an excision plasmid prophage and a chromosomally integrated prophage that becomes lytic in plant infections. Mol Plant Microbe Interact. 24(4):458-68.
[2] Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crecy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Ruckert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V. (2005) The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. 33(17):5691-702.