Transcript Comparative Genomics: Vibrio spp.
Comparative Genomics:
Vibrio spp.
ICGEB Workshop Group 4 Albert Auguste, Reia Guppy, Amalia Hosein, Andrés López, Maria Jose Muňoz, Silvia Vasquez, Jerome Foster
Study organism
Vibrio spp. of anaerobic bacteria (curved rods) > 70 species, across 4 families symbiotic, communalistic, pathogenic at least 12 are important human pathogens (Vibrionaceae)
Study organism
Pathogenic species are major causative agents of several clinical illnesses in humans (gastroenteritis , wound infections w/ septicaemia) Transmission usually by consumption of raw/uncooked shellfish, or exposure to contaminated or warm sea water E.g. V. cholerae, V. parahaemolyticus, V. vulnificus
Study organism
Invasive infections such as that of V. cholerae may rapidly progress to death Patients w/ liver malfunction are at high morbidity & mortality risk (e.g. V. vulnificus) CDC, 2008: 131 per 100,00 lab-confirmed infections of Vibrio spp. in the U.S.
Study organism
Other Vibrio spp. are marine pathogens e.g.
V. Harveyi - pathogen of fish and invertebrates, including sharks, sea bass, seahorses, lobster, and shrimp V. splendidus inflicts disease and death in many marine species including fish, oysters, mussels, and scallops Non-pathogenic include V. fischeri,
V. logei
Vibrio genome organization
Project Objectives
Compare nonpathogenic vs. pathogenic Vibrio
spp.
similarities?
unique traits?
genome organization?
Methodology
Pairwise comparison between Vibrio spp. using ACT (Artemis Comparison Tool; Carver et al., 2005 )
V. fischeri as a “reference” species for all
comparisons basal in taxonomy & phylogeny* of Vibrio spp to other available complete genomes (based on 16s rRNA; Thompson et al., 2009) non-pathogenic in both humans & marine life
Methodology
Dataset of eight (8) complete & published Vibrio genomes each with 2 chromosomes ( I and II) WebACT used to generate sequence & blast comparisons (blastn only*) ACT used on local server for actual comparative analyses
Methodology
Total of 14 ACT runs (7 x 2 chromosomes), V. fischeri
(MJ11) vs.
V. cholerae (M66_2) V. cholerae (MJ_1236) V. harveyi (ATCC_BAA_1116) V. parahaemolyticus (RIMD 2210633) V. vulnificus (YJ016) V. Sp. Ex25 V. splendidus (LGP32)
R ESULTS
ACTs for Chromosome I
V. harveyi V. sp Ex25 V. cholerae MJ66 V. splendidus V. vulnificus V. cholerae MJ1236 V. parahaemolyticus
ACTs for Chromosome II
V. harveyi V. sp Ex25 V. cholerae MJ66 V. vulnificus V. cholerae MJ 1236 V. parahaemolyticus V.splendidus
Selected genes for comparison
TCP – encodes pili protein (pathogenicity island) toxR – virulence regulation rtxA – modulation of toxicity ompU – membrane protein assoc. with virulence Pili– genes associated with pili formation (responsible for attachment to epithelium) PutA – part of PutAB operon (osmotic tolerance)
Strain
Vibrio fischeri V. Cholerae (MJ1236) V. harveyi** V. parahaemolyticus V. vulnificus V. sp Ex25 V. splendidus V. cholerae (MJ66)
-
TCP
1 1 2 8 8 9
Pili
5 8 6 8
ompU Genes rtxA
1 1 1 1 1 1 1 1* 1 5 1 1 -
toxR
1 1 1 TABLE 1. Select genes for pathogenesis and virulence (chromosome 1) -
PutA
-
Strain
Vibrio fischeri V. Cholerae (MJ1236) V. harveyi** V. parahaemolyticus V. vulnificus V. sp Ex25 V. splendidus V. cholerae (MJ66)
-
TCP
1 1 2 8 8 9
Pili
5 8 6 8
ompU Genes rtxA
1 1 1 1 1 1 1 1* 1 5 1 1 -
toxR
1 1 1 TABLE 1. Select genes for pathogenesis and virulence (chromosome 1) -
PutA
-
Strain
Vibrio fischeri V. Cholerae (MJ1236) V. harveyi** V. parahaemolyticus V. vulnificus V. sp Ex25 V. splendidus V. cholerae (MJ66)
-
TCP
1 1 2 8 8 9
Pili
5 8 6 8
ompU Genes rtxA
1 1 1 1 1 1 1 1* 1 5 1 1 -
toxR
1 1 1 TABLE 1. Select genes for pathogenesis and virulence (chromosome 1) -
PutA
-
Strain
Vibrio fischeri V. Cholerae (MJ1236) V. harveyi** V. parahaemolyticus V. vulnificus V. Sp Ex25 V. splendidus V. cholerae (MJ66)
-
TCP
2 3 1` 2 -
Pili
1 1 -
ompU Genes rtxA
2 -
toxR
1 -
PutA
1 1 TABLE 2. Select genes for pathogenesis and virulence (chromosome 2)
Strain
Vibrio fischeri V. Cholerae (MJ1236) V. harveyi** V. parahaemolyticus V. vulnificus V. Sp Ex25 V. splendidus V. cholerae (MJ66)
-
TCP
2 3 1` 2 -
Pili
1 1 -
ompU Genes rtxA
2 -
toxR
1 -
PutA
1 1 TABLE 2. Select genes for pathogenesis and virulence (chromosome 2)
CDSs
(at 100% Identity)
showing reassortment (V. Fischeri
vs
V. Cholerae M66)
Chrom. 2: Bifunctional protein PutA, absent in
V. sp Ex25 (possibly reassorted & pseudogeneized?)
Limitations
Only pairwise comparisons possible time constraints Inexperience with software e.g.
CDS key queries - “PutA” vs “puta” Tblastx run error (WebACT) – only Blastn used
C ONCLUSIONS Seems to be numerous reassortments among Vibrio spp. in comparison to V. fischeri Genomes very similar but “messy” (reassortments, duplicated stretches of sequence) Common gene products across all species, e.g. pilus associated genes Toxin genes maintained across pathogenic species Group needs more practice in analyzing this kind of data (steep learning curve)!!
A CKNOWLEDGEMENTS All the module instructors (esp. Dr. Pain!) Organizers @ UWI, UNU-BIOLAC & ICGEB