Wednesday, October 15, 2008

Bacteriophages SPP1 contains two tail tube proteins produced by programmed translational frameshift

Origin and function of the two major tail proteins of bacteriophage SPP1. Auzat et al., Molecular Microbiology (2008) 70, 557-569

Bacteriophages are viruses that infect bacteria and are known to play roles in horizontal gene transfer. The majority of known bacteriophages have a head and long non-contractile tail that serves as a pipeline for phage genome delivery into bacterial cell. Here, the authors report that the tail tube of Bacillus subtilus bacteriaphage SPP1 is comprised of two proteins, gp17.1 and gp17.1* , that are produced by a translational frameshift. This mosaic construction of tail tube was found to be important for assembly of the functional tail tube, but its significance is not fully uncovered yet.

Previously, it was shown that the key event of phage DNA injection in bacterial cell is a rearrangement of the inner wall of the tail tube (EMBO J, (2007) 26, 3720-3728). In this article, the authors separated SSP1 tail proteins by SDS-PAGE and found a protein band which was not expected from phage DNA sequence. Protein sequencing analysis indicated that the unexpected protein designated gp17.1* has the same amino-terminal sequence as that of tail protein gp17.1. gp17.1* is 10 kDa larger than gp17.1. The tail tube is made up of these two proteins at the ratio of 1:3. Based on the molecular size of gp17.1* and the sequences of gene 17.1, authors postulated that 17.1* is produced by a translational frameshift. Using site-directed mutagenesis of coding sequence 17.1 with protein profile analysis of the mutant phages, authors found out that 5'-CCCUAA-3' sequence located at the end of coding sequence 17.1 was the frameshift position.

To get insight into the function of gp17.1*, the authors constructed mutant phages that have tail tubes comprised exclusively of gp17.1 or gp17.1* and analyzed their structures by electron microscopy. When phages are assembled under the condition which either gp17.1 or gp17.1* are exclusively expressed, significant numbers of tailless heads (capsids) are made. This suggests the 3:1 ratio of gp17.1 and gp17.1* is important for correct phage assembly. Interestingly, both mutant phages had infection activity. The length and flexibility of mutant tails composed of either gp17.1 or gp17.1* were identical to SSP1 wild-type tails. gp17.1*-specific tail has protrusions on surface while gp17.1-specific tail has smooth surface. Authors postulate that carboxyl-terminus of gp17.1* causes protrusions on tail surface which facilitate initial contact of phages and attachment to the bacterial surface, while gp17.1 is ensures correct assembly of tail tube.

The potential translational frameshift site producing a carboxyl-terminus extension in a protein are also found in other phage surface protein genes (Mol Microbiol. (2003) 50, 303-317). Why do phages need two types of surface proteins which are identical except the carboxyl end extension of one of the proteins? What is the significance of strict ratio of the two proteins? Why is this the best strategy for phages? What is the target of the protrusion on tail tube surface? These are still interesting mysteries. It might be interesting to compare the host ranges of mutant phages that have either one of the two surface proteins.

Origin and Function of the Two Major Tail Proteins of Bacteriophage SPP1. Auzat I, Dröge A, Weise F, Lurz R, Tavares P. Molecular Microbiology (2008) 70: 557-569

Structure of bacteriophage SPP1 tail reveals trigger for DNA ejection. Plisson C, White HE, Auzat I, Zafarani A, São-José C, Lhuillier S, Tavares P, Orlova EV,
EMBO J (2007) 26:3720-8.

Genome and proteome of Listeria monocytogenes phage PSA: an unusual case for programmed + 1 translational frameshifting in structural protein synthesis. Zimmer M, Sattelberger E, Inman RB, Calendar R, Loessner MJ., Molecular Microbiology. (2003) 50:303-317.

Hirokazu Yano (university of idaho)

Tuesday, October 7, 2008

Type 3 fimbriae, encoded by the conjugative plasmid pOLA52, enhance biofilm formation and transfer frequencies in Enterobacteriaceae strains

Mette Burmølle, Martin Iain Bahl, Lars Bogø Jensen, Søren J. Sørensen and Lars Hestbjerg Hansen
Microbiology (2008), 154, 187–195

In this paper researchers from University of Copenhagen and The National Food Institute in Denmark bring our attention to a conjugative plasmid pOLA52 which features and genetic content occurred to be disturbing as they regard human and animal health.
pOLA52 plasmid was first isolated from swine manure and was shown to encode multidrug efflux pump which provides resistance to many antimicrobial agents such as olaquindox (which was or still is commonly used as a growth factor in pig farming), chloramphenicol, ethidium bromide, other antibiotics, detergents and disinfectants. It also carries
bla gene conferring resisitance to β-lactam antibiotics, such as ampicilin. Apart from multidrug resistance, pOLA52 plasmid carries 5.6 kb operon consisting of five genes, homologous to mrkABCDF genes contained in the mrk operon of Klebsiella pneumoniae, encoding type 3 fimbriae, which are known to be involved in attachment of bacteria to different kinds of biotic and abiotic surfaces, and thus increased biofilm formation.
Authors of the paper have previously observed that E. coli CSH26 strain harbouring pOLA52 plasmid formed higher amounts of biofilm and thus wanted to investigate if the operon conferring type 3 fimbriae could be responsible for observed feature.
In this study authors randomly introduced entranceposon pENTRANCEPOSON (KanR) into pOLA52 plasmid, electroporated it into E. coli Genehogs, selected tranformants on Kan and checked their ability to form biofilms on urinary catheters. Some clones occured to be biofilm negative and sequencing revealed that inserts were located inside type 3 fimbriae operon. Not surprisingly, biofilm positive clones had the inserts outside the operon.
Researchers have checked expression of mrk genes with RT-PCR and showed with immunoblotting that biofilm positive clones expressed type 3 fimbriae, whereas biofilm negative did not.
Later, they have conducted conjugation of pOLA52 plasmid into potentially pathogenic Enterobacteriaceae strains (such as Klebsiella pneumoniae, Salmonella typhimurium, Kluyvera sp., Enterobacter aerogenes) and tested the ability of transconjugants to form biofilms. It occured that transconjugants harbouring plasmid with transposon inside mrk operon showed significantly lower rate of plasmid transfer comparing to strains carrying wild type plasmid. Futhermore, transconjugants harbouring wild type pOLA52 plasmid formed biofilms, whereas strains with operon mrk mutated plasmid showed much lower biofilm formation.
This study proves how important and potentially dangerous pOLA52 plasmid is, as it can be transferred via conjugation to other bacteria, including pathogenic strains, providing them with new antibiotic resistances and type 3 fimbriae increasing their ability of spread plasmids and to form biofilms. Those newly accuaired features can lead to higher antibiotic persistence and increased spreading of pathogens on biological surfaces, such as tissues, as well as abiotic ones, for example catheters or artificial heart valves.
As pOLA52 plasmid is the first of probably many more plasmids with similar genetic content, there is a risk that one day they could be used as another dangerous weapon in hands of pathogenic bacteria. Let's hope we will be well prepared if this day would come...

Sylwia Deneka
Visiting Scholar
University of Idaho

Wednesday, October 1, 2008

What a man can make …….


Genome Transplantation in Bacteria: Changing One Species to Another
Carole Lartigue, John I. Glass, Nina Alperovich, Rembert Pieper, Prashanth P. Parmar, Clyde A. Hutchison III, Hamilton O. Smith, and J. Craig Venter 2007. Science 317, 632.

Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasmagenitalium Genome.
Daniel G. Gibson, Gwynedd A. Benders, Cynthia Andrews-Pfannkoch, Evgeniya A. Denisova, Holly Baden-Tillson, JayshreeZaveri, Timothy B. Stockwell, AnushkaBrownley, David W. Thomas, Mikkel A. Algire, Chuck Merryman, Lei Young, Vladimir N. Noskov, John I. Glass, J. Craig Venter, Clyde A. Hutchison III, Hamilton O. Smith 2008Published Online January 24, 2008 Science DOI: 10.1126/science.1151721

In these two papers, researchers from J. Craig Venter Institute in Rockville Maryland showed us the possibility of changing the entire genetic information of a living microorganism to create a new artificial organism.
In first paper they used two closely related Mycoplasmas: Mycoplasma mycoides large colony (LC) and M. capricolum. They used mycoplasma because of its specificity. Mycoplasmas do not have a cell wall, which makes them resistant to some therapeutic antibiotics like B-lactams. This also makes them more susceptible for uptake of different substances from the environment. One also cannot underestimate the biological importance of Mycoplasmas as pathogenic microorganisms, causing some nasty diseases in human and animals. Another interesting fact is that Mycoplasmas, compared to other bacteria, have relatively small genome, ranging from 0.6 to 1.4Mb. Up to now, 12 Mycolasma genomes have been completely sequenced and 11 more are in progress.
Small genome size and lack of the cell wall makes them ideal candidates for the genome “switching” experiment.
So, Carole Lartigue with coworkers took the large colony of M. mycoides and prepared intact genomic DNA in the way usually used for PFGE (pulsed field gel electrophoresis). All proteins were removed by proteinase treatment. This purified DNA was used for transformation of M. capricolum strain. After a few days some transformants grew on selective media. These transformants had genetic markers specific for donor strain but no sign of host specific markers was detected. That means that it is possible to replace a whole genome, at least using closely relative bacteria.
Cloning large genomic fragments is not a technical problem. Some bacterial artificial chromosome (BAC) clones already contain inserts of about 300kb in size. Such clones can be easily introduced into E. coli cells by electroporation. Using some specific recombination systems it could be possible to join two or three large clones inside E. coli cells to generate single DNA molecule, then isolate such a genome and introduce it into a new bacterial host.
But there is another way to build an entire genome. In second of the presented papers, the authors described this alternative way. They split the whole Mycoplasma genitalium genome into 101 cassettes, each of about 5000-7000bp. Those cassettes were chemically synthesized by three companies. All cassettes have specific overlapping sequences so they can be stuck together. The in vitro recombination event yielded intermediate assembliesof approximately 24 kb, 72 kb ("1/8 genome"), and 144 kb ("1/4genome"), which were all cloned as bacterial artificial chromosomes(BACs) in The complete synthetic genomewas assembled by transformation-associated recombination (TAR)cloning in the yeast Saccharomycescerevisiae, then isolatedand sequenced. This method allowed construction of an entire “artificial” bacterial genome.
Mycoplasmas have small genomes, but we already know some bacteria with even smaller genomes. The amphid endosymbiont Buchnera aphidicola genome consists of ~422kb, but a psyllidendosymbiont, Carlsonella ruddii, has even smaller genome (~160kb). Such small genomes are specific for pathogenic and especially endosymbiotic style of life. These bacteria reduce their genomes by deleting genes that are not necessary, like some anabolic pathways. On the other hand, they keep genes that are useful for themselves and for their hosts. These genes encode basic functions like replication, transcription and translation, as well as some of the biosynthetic pathways encoding for amino acids, cofactors and other essential compounds that their host cannot obtain from their diet. Surprisingly, also lots of genes encoding transport (uptake) systems have been eliminated.
Studying such small genomes we can learn which genes are really core genes and cannot be removed from the genome and which genes are not necessary. Furthermore, we can induce such big reductions in larger bacterial genomes. Analysis of these data as well as data obtained from analysis of the eukaryotic organelle (mitochondria and plastids) genomes could be used to construct an artificial endosymbiont.
Perhaps, it could be possible to make a new endosymbiont,which could be specific for some body tissue like liver or pancreas. They could live inside the cell,producingspecific proteins like insulin, clotting factors or other factors deficient in genetic diseases. This is fantasy but who knows the future…….

Additional articles:
S. G. E. Andersson 2006. TheBacterial World Gets Smaller. Science 13, pp.: 259 – 260.

A. I. Nilsson,S. Koskiniemi,S. Eriksson,E. Kugelberg,J. C. D. Hinton,D. I. Andersson 2005, Bacterial genome size reduction by experimental evolution. Proc. Natl. Acad.Sci. 102, pp.: 12112-12116.

Quanzhou Tao and Hong-Bin1998 Zhang 1998 Cloning and stable maintenance of DNA fragmentsover 300 kb in Escherichia coli with conventional plasmid-based vectors. NAR 26, 21, pp.: 4901-4909.

dr Jaroslaw Krol