Genomic Exploration of Produce Degradation 5
The issue of pathogenicity or virulence is always a priority for pathogen research.
In the pregenomics era, many virulence genes (e.g., those involved in plant cell wall
degradation, enzyme regulation, and export) were isolated by transposon mutagen-
esis (Hinton et al., 1989; Py et al., 1998). The role of these genes was later confirmed
using simple plant assays such as stem or tuber inoculation tests, often with artifi-
cially high concentrations of bacterial cells. The question is whether such conventional
approaches can identify genes expressed only under natural infection conditions. The
answer to this question relies on the techniques that can comprehensively analyze
every gene in the bacterial genome. Incidentally, this is one of the goals of genomic
research.
Whole genome sequence comparison of different soft rot erwinia strains can
identify candidate genes for pathogenicity and host specificity. The potential can be
seen in the examples of Xanthomonas and Xylella. Da Silva et al. (2002) compared
the complete genome sequences of Xanthomonas axanopodis subsp. citri and Xan-
thomonas campestris pv. campestris. The two genomes shared more than 80% of
their genes. Gene order is conserved along most of their respective chromosomes.
Such a high genetic similarity contrasts with their distinct disease phenotypes and
host ranges. Xanthomonas axanopodis subsp. citri is the pathogen that causes citrus
canker, and Xanthomonas campestris pv. campestris causes black rot in crucifers.
Sequence comparison identified a set of strain-specific genes, some of which
are probably responsible for the distinct pathogenicity and host specificity profiles.
Both Xanthomonas axanpodis pv. citri and Xanthomonas campestris pv. campestris
have an extensive repertoire of genes for cell-wall degradation. Both genomes code
for enzymes with cellulolytic, pectinolytic, and hemicellulolytic activities. Xanth-
omonas campestris pv. campestris has more genes involved in pectin and cellulose
degradation than Xanthomonas axanpodis pv. citri. In addition, Xanthomonas
campestris pv. campestris has two 1,4-b-cellobiosidases and two pectin esterases,
none of which are found in Xanthomonas axanopodis pv. citri. The differences in
symptoms may be correlated to the noted differences in genes for cell-wall degra-
dation. These differences suggest that Xanthomonas campestris pv. campestris is
uniquely suited to invade and colonize host tissue, a fact that may partially explain
the systemic nature of its infection. In contrast, Xanthomonas axanpodis pv. citri
induces a strong local response with cell proliferation and necrosis but shows little
spontaneous dissemination, probably due to a smaller number of genes capable of
causing a massive degeneration of host tissue (da Silva et al., 2002).
Genome comparison of two X. fastidiosa strains revealed a different picture with
regard to population genomics. Van Sluys et al. (2003) reported the genome sequence
of X. fastidiosa (Temecula strain), isolated from a naturally infected grapevine with
Pierce’s disease in California. Comparative analyses with a previously sequenced
X. fastidiosa strain 9a5c responsible for citrus variegated chlorosis revealed that 98%
of the X. fastidiosa Temecula genes are shared with the X. fastidiosa strain 9a5c
genes. Furthermore, the average amino acid identity of the open reading frames in
the two strains is 95.7%. Genomic differences are limited to phage-associated chro-
mosomal rearrangements and deletions that also account for the strain-specific genes
present in each genome. Genomic islands, one in each genome, were identified.