Chlorella virus genome

Viscomi, V. Sangiorgio, C. Pagliuca, T. Meckel, F. Horvath, S. Gazzarrini, P. Valbuzzi, J. DiFrancesco, and G. FEBS Lett. Nandhagopal, N. Simpson, J. Gurnon, X. Yan, T. Baker, M. Graves, J. The structure and evolution of the major capsid protein of a large, lipid-containing, DNA virus.

Petrik, D. Iseli, B. Montelone, J. Van Etten, and R. Improving baculovirus resistance to UV inactivation: Increased virulence resulting from expression of a DNA repair enzyme. Pathology Roberts, R. A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes. Nucleic Acids Res. Tonetti, M. Zanardi, J. Gurnon, F. Fruscione, A. Armirotti, G. Damonte, L. Sturla, A. De Flora, and J. Rothermel, T. Meckel, J. Van Etten, A. Moroni, and G.

Severino, M. Lombardi, M. Morandi, D. Di Francesco, J. Van Etten, G. The viral potassium channel Kcv: structural and functional features.

Gazzarrini, and J. Are chlorella viruses a rich source of ion channel genes. Van Etten, J. Unusual life style of giant chlorella viruses. The chlorella viruses have several unusual features in addition to their large genome size and we are focusing on two of these unusual properties: i. The chlorella viruses, unlike all other viruses, encode most, if not all, of the machinery involved in the glycosylation of their major capsid proteins. In collaboration with Purdue scientists we have solved the structure of the virus major capsid protein and identified six glycosylation sites.

The chlorella viruses are the first viruses to encode a protein that forms a functional, potassium ion channel. Expression of the channel in Xenopus oocytes, human kidney cells and CHO cells produced K-selective, voltage-sensitive currents. The virus encoded protein only 94 amino acids is the smallest known potassium ion channel protein. These experiments are being done in collaboration with two electrophysiology laboratories in Europe. Impacts Viruses that infect fresh water chlorella-like green algae are common throughout the world.

These viruses contain more genes than any other known virus. Furthermore, some of these virus genes encode medically important proteins. Publications Gazzarrini, S. Membrane Biol. Castberg, T. Isolation and characterization of a virus that infects Emiliania huxleyi Haptophyceae. Phycology Fortune, J. Biochemistry Morehead, T. Ornithine decarboxylase encoded by chlorella virus PBCV Genus Chloroviruses Phycodnaviridae.

In: The Springer Index of Viruses. Tidona and G. Darai eds. Springer-Verlag, Berlin. Phycodnaviridae - large DNA algal viruses. The chlorella viruses have several unusual features in addition to their large genome size and we are focusing our research efforts on two of these unusual properties: i. The chlorella viruses, unlike that of all other viruses, code for most, if not all, of the machinery envolved in the glycosylation of their major capsid proteins.

In collaborations with other laboratories, we are trying to solve the structure of the glycan and also trying to identify the viruses encoded genes involved in the process. The channel has been expressed in Xenopus oocytes and human kidney cells. Futhermore, the virus encoded protein only 94 amino acids is the smallest known potassium ion channel protein.

These properties are listed in Supplementary material 1. The predicted p I s of the proteins are depicted in Fig. Despite a trend for the proteins to have a p I in the 10—11 pH range, a peak also occurs at pH 4. Therefore, some of the ATCV-1 basic proteins are probably associated with the virion where they presumably help neutralize the positively charged genomic DNA. However, the functions of the proteins that have p I s in the 4.

Seventy-three percent of the major ORFs are separated by less than nucleotides. No ATCV-1 gene products have been tested for activity. However, we assume that any ATCVencoded proteins that have functional homologs in the other chlorella viruses are also functional.

Map of the ATCV-1 genome arranged in a circle. However, the genome is a linear molecule and the ends are depicted at the top of the figure as green lines L and R represent the left and right ends of the genome, respectively. The predicted ORFs are shown in both orientations and colored according to their functional category. The ORF ZR has been classified as a putative replication factor C due to its similarity to replication factor C's identified in other chlorella viruses.

Some of these homologs, e. The ATCV-1 proteins are more similar to their homologs from other organisms than they are to each other. This finding suggests that the viral PCNA genes did not arise by a recent gene duplication.

No recognizable RNA polymerase components have been detected in any of the chlorella viruses that have been sequenced, including ATCV This observation supports the concept that infectious viral DNAs are targeted to the nucleus and that host RNA polymerase s initiate s viral transcription, possibly in conjunction with virion-packaged transcription factors.

Except for the superfamily II helicase domains, the two proteins do not resemble one another. It is not known how this process occurs, but histone methylation may be involved in inhibiting host transcription.

Both proteins are also implicated in chromatin remodeling Kim and Clark, This observation suggests that either some of the viral transcripts or host transcripts may undergo some post-transcriptional editing Gerber and Keller, ATCV-1 has several genes that encode proteins involved in post-translational modifications, including prolylhydroxylase ZR , protein kinases see below , and glycosyltransferases see below. Additionally, the virus encodes three proteins involved in protein degradation, ubiquitin ZL , ubiquitin C-terminal hydrolase ZR , and ring finger ubiquitin ligase ZL.

The remaining 5 tRNAs have homologs in at least two additional chlorella viruses. Although the orientation of the tRNA genes is the same in all six viruses, their order and location vary between the viruses.

Typically, these three nucleotides are added post-transcriptionally. Codon usage analyses of viral-encoded proteins indicate a strong correlation between the abundance of the virus-encoded tRNAs and their usage in viral proteins.

Note that the percent identity is expressed out of 13 nts even though the ATCV-1 intron contains 10 nts. ATCV-1 encodes 11 enzymes involved in nucleotide metabolism. ATCV-1 also encodes a ribonucleoside-triphosphate reductase ZL , which is the first time a gene encoding this enzyme has been found in the chlorella viruses.

Instead, the viruses encode a protein that is a member of a newly recognized family of flavin-dependent thymidylate synthetases, named ThyX Graziani et al.

Preliminary studies indicate that ATCV-1 Kcv complements a yeast mutant lacking a potassium ion channel Kang, unpublished results.

ATCV-1 has 13 genes that encode proteins with high identities to enzymes involved in either manipulating sugars, synthesizing polysaccharides, or transferring sugars to proteins. Furthermore, some of the viruses encode enzymes involved in synthesizing the sugars that comprise the polysaccharides, e. Unlike many of the other chlorella viruses, ATCV-1 does not encode hyaluronan synthase or chitin synthase homologs.

Furthermore, ATCV-1 is the first chlorella virus to lack a glutamine:fructosephosphate amidotransferase encoding gene. ATCV-1 encodes six putative glycosyltransferases Table 2 which are probably involved in glycosylation of the virus major capsid protein Graves et al. This is the most glycosyltransferases encoded by any chlorella virus sequenced to date. ATCV-1 encodes six proteins that may be involved in degrading cell walls either during virus infection or virus release.

Chlorella viruses contain different levels of 5-methylcytosine 5 mC and N 6 -methyladenine 6 mA in their genomes Van Etten et al. The level of methylation in the ATCV-1 genome is unknown. Therefore, the methylation of the ATCV-1 genome is expected to be low. Homing endonucleases are rare DNA-cleaving enzymes that are typically encoded by introns and inteins and the chlorella viruses encode many of these enzymes. Homing endonucleases are classified into four families Belfort and Roberts, None of the chlorella virus-encoded homing endonucleases has been tested for activity.

Therefore, it is unknown if they have an essential role in the replication cycle. The Tlr 6Fp DNA mobile protein is encoded by a member of a family of genetic elements limited to Tetrahymena thermophila Wuitschick et al. PBCV-1 was the first virus reported to have genes encoding polyamine biosynthetic enzymes, including two pathways to synthesize putrescine. ODC catalyzes the first and rate-limiting step in polyamine biosynthesis, the decarboxylation of ornithine to putrescine Davis et al.

The plotted values are of instantaneous current I i , measured 3 ms after the voltage step. Effect of a mutation in the selectivity filter on conductance and permeability to rubidium. Measurements performed in oocytes by a two-electrode voltage clamp, applying the standard voltage protocol see the Experimental section and in the presence of 50 mM external KCl squares or RbCl circles.

A The Figure includes a set of data already displayed in Figure 3 B. Permeability and conductance of wild-type and mutant channels to different univalent cations. All cations were 50 mM as chloride salts. The aforementioned results imply that the cations interact with the channel protein. Hence permeation through Kcv channels is more complex than predicted by constant field theory. For this reason the E rev value alone is not sufficient to provide an absolute measure of Kcv channel permeability.

We also estimated the conductance of the channel for different ions away from equilibrium [ 22 ]. Finally it has to be mentioned that the kinetics of the channel change as a consequence of the transported substrate.

This kinetic effect was not analyzed further in the present study. Figure 4 A shows that, in selective conditions 0.

It abolishes the inward current and also slightly affects the outward current. The plotted values of fractional current, I f , could be fitted by the Hill equation as follows:.

Since the best fit of n was between 1. Owing to the voltage-dependent nature of the block, the apparent K d obtained from the dose—response curves varies in a linear fashion with voltage when plotted in a semi-logarithmic scale Figure 4E.

The extrapolated value of K d at 0 mV was 0. Collectively these data show that the smaller version of a Kcv-type channel behaves similarly to its larger orthologues. Moroni, unpublished work. The K d value is strongly voltage-dependent and decreases e-fold for 31 mV hyperpolarization. However, this amino acid alone cannot explain the entire selectivity. However, the data also indicate that the overall selectivity of a filter can only be understood in the context of other structural parts of the channel protein.

Even though the monomer is only 82 amino acids long it still forms a tetramer. All of these functional features must be inherent in the basic structure of this miniature channel protein.

National Center for Biotechnology Information , U. Biochem J. Author manuscript; available in PMC Jul Kast , 3 Gerhard Thiel , 4 and Anna Moroni 1. A Find articles by Ming Kang.

James L. A Find articles by James L. Stefan M. Author information Copyright and License information Disclaimer. Corresponding author: A. Moroni, ti. Copyright notice.

The publisher's final edited version of this article is available at Biochem J. See other articles in PMC that cite the published article. Introduction Phycodnaviruses [ 1 — 4 ] consist of a genetically diverse, but morphologically similar, group of large dsDNA double-stranded DNA -containing viruses — kb that infect algae from both fresh and marine waters [ 5 , 6 ]. DNA sequence analysis of the kbp genome of Paramecium bursaria chlorella virus 1 PBCV-1 , the prototype of this virus family Phycodnaviridae , predict approximately protein-encoding genes and 11 tRNA genes.

In addition, the chlorella viruses have several features and encode many gene products that distinguish them from most viruses.