Investigation of the Potyviridae on secondary structures

Sonja Karam and Franziska Heinze

About the Potyviridae
Implementation
Results - Potyviruses
Results - Bymoviruses
Links and References

About the Potyviridaeerwendete

Taxonomic Structure of the Family

Family 00.057. Potyviridae
Genus 00.051.0.01. Potyvirus
Genus 00.057.0.05. Ipomovirus
Genus 00.057.0.04. Macluravirus
Genus 00.057.0.02. Rymovirus
Genus 00.057.0.06. Tritimovirus
Genus 00.057.0.03. Bymovirus

Inclusions of *Potyviridae* Found In Florida The Potyviridae family has six genera. All the virus species listed below belong to the Potyvirus Genus .
Virus species	Inclusion	Virus species	Inclusion
*alstroemeria mosaic*		*peanut mottle*
*Araujia mosaic*		*pepper mottle* (DPI)
*bidens mottle* in zinnia (IFAS Extention)		potato A
*bean common mosaic* (also peanut stripe)		*potato Y* (DPI)
*bean yellow mosaic* in Vicia faba (picture scanned from monograph 9)		*pokeweed mosaic*
*cardamom mosaic*		*Ranunclulus mottle*
*celery mosaic in Apium graveolens* pictures scanned from monograph 9	About the Potyviridae	*soybean mosaic*
*clover yellow vein*		*sugarcane mosaic*
*commelina mosaic*		*sweet potato feathery mottle*
*Crinum mosaic*		*Tradescantia/* *Zebrina mosaic*
*Dasheen mosaic*	nclusions of *Potyviridae* Found In Florida The Potyviridae family has six genera. All the virus species listed	*tobacco etch*
*Desmodium mosaic*		*tulip breaking*
*Dioscorea green banding mosaic*
*Hippeastrum mosaic*		*turnip mosaic*
*lettuce mosaic* in Lactuca sativa		*Vanilla necrosis* in Vanilla spp
*maize dwarf mosiac* in Zea mayis		*watermelon* *mosaic*
*onion yellow dwarf* in Allium cepa		*watermelon leaf mottle*
*papaya ringspot* in Cucurbita pepo		*zucchini yellow mosaic* in squash

Potyvirus Cylindrical Inclusions Potyviruses have been classified into four groups based on the morphology of their cylindrical inclusion in the electron microscope. On the left are picutes taken in the transmission electron microscope of each of the four cylindrical inclusion types in thin sections of tissue . On the right are pictures taken in the light microcope.of the same type of inclusions in leaf stips stained with the OG stain.

Subdivision I - Pinwheels and Scolls

Subdivision II - Pinwheels and Laminated Aggregates

Subivision III - Pinwheels, Scolls and Laminated Aggregates

Sudivision IV - Pinwheels, Scolls, and short Curved Laminated Aggregates

Potyvirus

The potyvirus genus has approximately 180 members making it the largest recognized group of plant viruses. It has one of the widest host ranges of all virus groups. Potyviruses occur worldwide but are prevalent in tropical and subtropical regions. They infect monocotyledonous species and are one of the most destructive viruses of cash crops. Viruses in this classification have a helical structure that forms long filaments.

Potyvirus Vectors

The potyvirus is transmitted mechanically by aphid mouth parts in a non-persistant, non-circulative, stylet borne manner. Aphids can obtain the virus after only brief contact with an infected host and usually retain the virus for less than an hour, though a few viruses can survive up to 40 hours. Because of the brief retention of the virus, aphids can normally only carry it for relatively short distances. However, with strong winds the virus can be spread great distances from other infected hosts. One speculation of how aphids retain the virus is that during feeding the virus adheres to the sucking pump and foregut. In subsequent feedings sap from the foregut is regurgitated, carrying the virus to a new host. Transmission of the virus by aphids is dependent upon a helper component protein HC-Pro which facilitates binding of virus particles to the aphid's maxillary stylets. Aphid transmissibility and specificity are also dependent upon the coat protein. Some potyviruses can also be seed transmitted depending on the virulence of the virus, age of the plant, and environmental conditions.

Horseradish plant infected with TuMV (a potyvirus)

Life cycle

After the aphid deposits the virus on the host, it enters the cell and the coat protein is removed. A replicase is then assembled and the virus is copied many times. Some of these copies remain as uncoated RNA molecules and move into adjacent cells to promote further infection. Primary infection then occurs when other copies are coated with the protein and ascend into the upper regions of the plant without causing serious harm to the plant. These virus particles remain in the upper regions throughout the vegetative cycle of the plant. Upon completion of this cycle the virus descends to the tubers for hibernation until spring. Once the tubers germinate the virus is activated and secondary infection takes place throughout the whole plant. This secondary infection causes more physical damage to the plant and is now capable of being transmitted to other healthy plants by aphids or other vectors.

Potyvirus Genome

Potyviruses are non-enveloped and contain positive-sense ssRNA of about 10 kb with a 3' poly A tail. The RNA genome contains one long ORF expressed as a 350 kDa polyprotein precursor that is eventually cleaved into several functional proteins, including HC-Pro and the coat protein. The coat protein forms disks of 7-8 subunits which are stacked into a helix with pitch of 3.3-3.4 nm. The resulting filaments are 680-750 nm in length. The coat protein contains DAG amino acid triplet at 2 locations and any mutation of these will result in a non-aphid transmissible virus. Another essential component of aphid transmissibility is the 53-58 kDa helper component protein, HC-Pro. HC-Pro functions as a dimer and is translated from an area located near the 5' end of RNA. HC-Pro aids in the binding of virus to the maxillary stylets. It also acts as a proteinase and is speculated to assist in cell to cell movement.

Implementation

General search for sequences of the family Potyvirdae from the data base NCBI: http://www.ncbi.nlm.nih.gov/

Alignment of the selected sequences with clustalW: http://ftp-igbmc.u-strasbg.fr/TopE.html

RNA fold with ViennaRNA package:http://www.tbi.univie.ac.at/RNA/

Search for reliably secondary structure and production of mountainplots with Alidot: http://www.tbi.univie.ac.at/RNA/ALIDOT

Results - Potyviruses

Used sequences:

We selected the following potyviruses for the determination of the secondary structures.Their score amounted to at least 60% .We did not regard further viruses haben, because the results of their pairwise alignments were not satisfyingly .

Sequence 1-Pepper mottle virus:             NC_001517
Sequence 2-Potato virus Y:                      NC_001616
Sequence 3-Potato virus V:                      NC_004010
Sequence 4-Wild potato mosaic virus:    NC_004426
Sequence 5-Peru tomato mosaic virus:    NC_004573

Pairwise alignments:

Sequences (1:2) Aligned. Score: 61
Sequences (1:3) Aligned. Score: 63
Sequences (1:4) Aligned. Score: 65
Sequences (1:5) Aligned. Score: 63
Sequences (2:3) Aligned. Score: 60
Sequences (2:4) Aligned. Score: 62
Sequences (2:5) Aligned. Score: 60
Sequences (3:4) Aligned. Score: 74
Sequences (3:5) Aligned. Score: 73
Sequences (4:5) Aligned. Score: 74

Mountainplot


	The green and blue ranges refer to conserved mutations, while the constant basepairs are shoen by the red sections. The larger the amplitude, the longer is the secondary structure in the appropriate range.

Determined secondary structures

The following graphs show the determined secondary structures: Paired positions with consistent mutations are shown by circles around the varying position, compensatory mutations by circles around both pairing partners and inconsistent mutants are indicated by gray instead of black lettering.

bp 3250 - 3350

bp 1640 - 1780

bp 9505 - 9545

Schritt

bp 330 - 390

bp 3100 - 3150

bp 3595 - 3675

bp 8202 -8255

bp 8600 - 8685

bp 4245 - 4340

Results - Bymoviruses

Used Sequences

Sequence 1-Wheat yellow mosaic virus RNA1:      NC_002350
Sequence 2-Barley yellow mosaic virus RNA1:      NC_002990
Sequence 3-Barley mild mosaic virus RNA1:          NC_003483
Sequence 4-Oat mosaic virus RNA1:                       NC_004016

Pairwise alignments:

Sequences (1:2) Aligned. Score: 68
Sequences (1:3) Aligned. Score: 40
Sequences (1:4) Aligned. Score: 62
Sequences (2:3) Aligned. Score: 44
Sequences (2:4) Aligned. Score: 62
Sequences (3:4) Aligned. Score: 47