Showing posts with label genome sequence. Show all posts
Showing posts with label genome sequence. Show all posts

Monday, March 21, 2016

The genomes of 20 species of Leptospira

A massive study describing the genomes of 20 species of Leptospira was published a few weeks ago in PLOS Neglected Tropical Diseases.  The deluge of sequence information will be valuable to those in the leptospirosis field.  Scientists will be able to examine differences in genetic content between various categories of Leptospira species to generate hypotheses for experimental testing.  For example, genes present in species that cause infections but missing in species that don't may be important factors responsible for the pathogenesis of Leptospira.  The genome information will also aid in vaccine and serodiagnostics development by allowing researchers to identify protein antigens that are conserved among Leptospira species circulating within a region of interest.

The 20 Leptospira species are divided into 14 infectious and six noninfectous species.  (Actually, there are now 22 species known but only 20 when this study was launched.)  The infectious species are divided further into nine pathogenic and five "intermediate" species based on their genetic relatedness.

The Venn diagram below shows the number of genes that are shared among and within the three categories of Leptospira and Leptonema illini, a closely-related spirochete.  Looking at the relevant intersection (overlap) in the diagram, there are 255 genes that are carried by infectious Leptospira but not by saprophytic Leptospira.  (The other two figures in the overlap are the number of shared genes tabulated using looser criteria.  In these cases there are 302 genes found in all but one infectious Leptospira and 369 genes when those found in the majority of infectious species are counted.)  Similarly, there are 109 genes unique to the pathogenic species (or 161 or 416, if you want to use less stringent criteria).  The small circles at the periphery show the number of genes unique to each species.  So for example, L. interrogans, the species favored for study in molecular biology labs, has 672 genes that are not found in any other Leptospira species.

Figure 2A from Fouts et al., 2016.  Source.

Reference

Fouts DE, Matthias MA, Adhikarla H, Adler B, Amorim-Santos L, Berg DE, Bulach D, Buschiazzo A, Chang YF, Galloway RL, Haake DA, Haft DH, Hartskeerl R, Ko AI, Levett PN, Matsunaga J, Mechaly AE, Monk JM, Nascimento AL, Nelson KE, Palsson B, Peacock SJ, Picardeau M, Ricaldi JN, Thaipandungpanit J, Wunder EA Jr, Yang XF, Zhang JJ, & Vinetz JM (2016). What makes a bacterial species pathogenic?: Comparative genomic analysis of the genus Leptospira. PLoS Neglected Tropical Diseases, 10 (2) PMID: 26890609

Sunday, January 3, 2010

E. coli-like genes in the spirochete Brachyspira hyodysenteriae, the agent of swine dysentery

The genus Brachyspira comprises at least seven species of anaerobic spirochetes that live in the large intestines of various birds and animals (including humans).  One species, Brachyspira hyodysenteriae, causes swine dysentery, a disease that causes economic loss among pig farmers worldwide.  Afflicted pigs produce loose stools covered with mucus and blood.  In severe cases, necrotic chunks of colon lining are expelled with the stool.

An Australian group sequenced the genome of B. hyodysenteriae strain WA1 to figure out how the spirochete thrives in the complex nutritional environment of the large intestine and induces swine dysentery.  They found 2,122 protein-coding genes distributed between a 3,000,694 bp chromosome and a 35,940 bp plasmid.  A number of genes encoded degradative enzymes such as proteases, phospholipases, and hemolysins that may or may not account for the damage to the colon observed in swine dysentery cases.  Otherwise, no obvious pathogenic mechanism for the disease process could be gleaned from the genome sequence.

Remarkably, half of the proteins encoded in the B. hyodysenteriae genome were most similar in sequence to proteins of Escherichia and Clostridium, genera that are not even on the same branch on the bacterial evolutionary tree as spirochetes.  A mere 6.4% of B. hyodysenteriae proteins matched best to proteins of other spirochetes.


From Table 3 of Bellgard 2009.

Among the Escherichia- and Clostridium-like genes, those encoding proteins involved with amino acid and sugar metabolism and transport were over-represented.  Since E. coli, Clostridium species, and B. hyodysenteriae all live in the large intestine, the similarity in the proteins may simply reflect convergent evolution that enable the bacteria to metabolize the nutrients available in the colon.  The more attractive possibility is that B. hyodysenteriae acquired the genes from the other enteric bacteria by horizontal gene transfer thereby allowing the spirochete to adapt to the complex nutritional environment of the large intestine.  At least for the E. coli-like genes, examining their GC content may help distinguish between the two possibilities since the GC content of B. hyodysenteriae is only 27% versus 50% for E. coli.

How can B. hyodysenteriae acquire genes from other enteric bacteria?  A commentary in the journal Gut Pathogens raised the possibility that bacteriophage-like elements found in the B. hyodysenteriae genome could be involved, although bacteriophages generally do not transfer DNA between different species of bacteria.  Another possibility is that genes could be acquired from other bacteria by conjugation, a form of microbial mating.  Although the capacity of B. hyodysenteriae for acquiring DNA from other bacteria by conjugation is unknown, scientists have demonstrated that another spirochete could acquire DNA from E. coli by conjugation in the laboratory setting.

Image source

Sow with piglet, from Wikipedia

References

Bellgard, M.I., Wanchanthuek, P., La, T., Ryan, K., Moolhuijzen, P., Albertyn, Z., Shaban, B., Motro, Y., Dunn, D.S., Schibeci, D., Hunter, A., Barrero, R., Phillips, N.D., and Hampson, D.J. (2009).  Genome sequence of the pathogenic intestinal spirochete Brachyspira hyodysenteriae reveals adaptations to its lifestyle in the porcine large intestine.  PLoS ONE 4(3):e4641. DOI: 10.1371/journal.pone.0004641

Hampson, D.J. and Ahmed, N. (2009).  Spirochaetes as intestinal pathogens:  Lessons from a Brachyspira genome.  Gut Pathogens 1(1):10.  DOI: 10.1186/1757-4749-1-10

Monday, December 28, 2009

Leptospira and E. coli caught in the act

I found this web photo of E. coli mating with the spirochete Leptospira biflexa in a process called conjugation (image source, Mathieu Picardeau, Pasteur Institute).  The donor E. coli cell is transferring a copy of a plasmid bearing antibiotic resistance genes to the recipient spirochete.  The DNA is most likely pushed through a pore that forms between the mating pair where the outer membranes come together.


There are many types of plasmids, but only self-transmissible plasmids are capable of transferring copies of themselves to other bacteria by conjugation. These plasmids carry a set of at least 20 genes collectively called tra (transfer), which encode all of the proteins necessary to carry out conjugation.  The conjugational proteins assemble into several structures, including the sex pili, which bring the mating pair together, the relaxosome, which processes the DNA for transfer, and the poorly characterized pore through which the DNA traverses.  The plasmids can also harbor additional genes that have no role in conjugation, including genes encoding resistance to antibiotics.  RP4 is one example of a self-transmissible plasmid that can transfer itself to a wide range of bacteria species.  Self-transmissible plasmids have been found in many different bacteria, yet none have been discovered in spirochetes.

Transformation is the microbiologist's favorite genetic tool for delivering DNA of their choosing into bacteria. Unfortunately for those interested in leptospirosis, transformation of disease-causing species of Leptospira such as L. interrogans is difficult.  Conjugation employing a laboratory strain of E. coli as a donor provides scientists another route for delivering DNA into Leptospira.  For example, the plasmid illustrated below (Figure 1 from Picardeau, 2008) has been used to ferry the Himar1 transposon into Leptospira for random insertional mutagenesis.  Many readers may be most familiar with the F conjugational plasmid of E. coli, but the conjugational machinery found on the RP4 self-transmissible plasmid is used here since it is able to deliver DNA to a wide range of bacteria species.

Figure 1 from Picardeau, 2008.  The Himar1 transposon consists of the arrowheads and everything in between, including the kanamycin-resistance gene (KmR).  The RP4 oriT element and the genes encoding the C9 tranposase and spectinomycin resistance (SpcR) lie outside of the transposon.


The critical element of the plasmid is the RP4 oriT sequence where relaxase, a component of the relaxosome, nicks the DNA to initiate the transfer process.  The tra genes were removed to permit easy manipulation of the plasmid.  To perform conjugation, the plasmid was transformed into a special E. coli strain that encodes the RP4 tra genes on its chromosome.  The E. coli cells were then mixed with Leptospira and concentrated onto a filter to facilitate mating.  After allowing them to mate for 20 hours, the mating mixture was plated onto Leptospira medium agar plates containing the antibiotic kanamycin to recover Leptospira mutants with the transposon on one of its two chromosomes.  The plasmid itself is unable to replicate in Leptospira, so the transposon must hop onto a chromosome following plasmid transfer to enable growth of kanamycin-resistant Leptospira into colonies.  The donor E. coli bacteria had been genetically modified to require the nutrient diaminopimelate (DAP) to counterselect the donor on the agar plates, which were lacking DAP.

It is not feasible to screen L. interrogans insertion mutants for a desired phenotype (trait) following a single mating experiment since only a few hundred kanamycin-resistant colonies can be recovered.  Tens of thousands of mutants would be necessary to ensure coverage of (almost) all L. interrogans genes.

One application of this genetic tool is to perform multiple mating experiments to generate a library of mutants with insertions of Himar1 in different L. interrogans genes.  The sequence of the insertion site of the transposon in the chromosome can be obtained easily with today's sequencing technology.  Further experiments can be performed to examine any mutants with insertions in genes that hold the investigator's interest.  Several labs have teamed up to embark on a similar approach by delivering the Himar1 transposon into L. interrogans by transformation (see the Murray 2009 paper), which does not yield as many colonies as conjugation.

References

Picardeau, M. (2008).  Conjugative transfer between Escherichia coli and Leptospira spp. as a new genetic tool.  Applied and Environmental Microbiology 74(1):319-322.  DOI: 10.1128/AEM.02172-07

Murray G.L., Morel, V., Cerqueira G.M., Croda, J., Srikram, A.,  Henry, R., Ko, A.I., Dellagostin, O.A., Bulach, D.M., Sermswan, R.W., Adler, B., and Picardeau, M. (2009).  Genome-wide transposon mutagenesis in pathogenic Leptospira species.  Infection and Immunity 77(2):810-816.  DOI: 10.1128/IAI.01293-08