Revolution of novel fungal genes

The evolution of novel fungal genes from non-retroviral RNA viruses

Derek J. Taylor and Jeremy Bruenn

BMC Biology 2009, 7:88doi:10.1186/1741-7007-7-88

Published:	18 December 2009

Abstract (provisional)

Background

Endogenous derivatives of non-retroviral RNA viruses are thought to be absent or rare in eukaryotic genomes because integration of RNA viruses in host genomes is impossible without reverse transcription. However, such derivatives have been proposed for animals, plants and fungi, often based on surrogate bioinformatic evidence. At present, there is little known of the evolution and function of integrated non-retroviral RNA virus genes. Here, we provide direct evidence of integration by sequencing across host-virus gene boundaries and carry out phylogenetic analyses of fungal hosts and totivirids (dsRNA viruses of fungi and protozoans). Further, we examine functionality by tests of neutral evolution, comparison of residues that are necessary for viral capsid functioning and assays for transcripts, dsRNA and viral particles.

Results

Sequencing evidence from gene boundaries was consistent with integration. We detected previously unknown integrated Totivirus-like sequences in three fungi (Candida parapsilosis, Penicillium marneffei and Uromyces appendiculatus). The phylogenetic evidence strongly indicated that the direction of transfer was from Totivirus to fungus. However, there was evidence of transfer of Totivirus-like sequences among fungi. Tests of selection indicated that integrated genes are maintained by purifying selection. Transcripts were apparent for some gene copies, but, in most cases, the endogenous sequences lacked the residues necessary for normal viral functioning.

Conclusions

Our findings reveal that horizontal gene transfer can result in novel gene formation in eukaryotes despite miniaturized genomic targets and a need for co-option of reverse transcriptase.

Emergence of Hepatitis C Virus Genotype 4: Phylogenetic Analysis Reveals Three Distinct Epidemiological Profiles

AMC Liver Center, Department of Gastroenterology and Hepatology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands,¹ Laboratory of Clinical Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands,² Cluster of Infectious Diseases, Amsterdam Health Service, Amsterdam, The Netherlands,³ Department of Internal Medicine, Academic Medical Center, University of Amsterdam, CINIMA, Amsterdam, The Netherlands,⁴ Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands⁵

Received 11 June 2009/ Returned for modification 19 August 2009/ Accepted 24 September 2009

Hepatitis C virus (HCV) genotype 4 (HCV-4) infection is considered to be difficult to treat and has become increasingly prevalent in European countries, including The Netherlands. Using a molecular epidemiological approach, the present study investigates the genetic diversity and evolutionary origin of HCV-4 in Amsterdam, The Netherlands. Phylogenetic analysis of the NS5B sequences (668 bp) obtained from 133 patients newly diagnosed with HCV-4 infection over the period from 1999 to 2008 revealed eight distinct HCV-4 subtypes; the majority of HCV-4 isolates were of subtypes 4d (57%) and 4a (37%). Three distinct monophyletic clusters were identified, with each one having a specific epidemiological profile: (i) Egyptian immigrants infected with HCV-4a (n = 46), (ii) Dutch patients with a history of injecting drug use infected with HCV-4d (n = 44), and (iii) Dutch human immunodeficiency virus (HIV)-positive men who have sex with men (MSM) infected with HCV-4d (n = 26). Subsequent molecular clock analyses confirmed that the emergence of HCV-4 within these three risk groups coincided with (i) the parenteral antischistosomal therapy campaigns in Egypt (1920 to 1960), (ii) the popularity of injecting drug use in The Netherlands (1960 to 1990), and (iii) the rise in high-risk sexual behavior among MSM after the introduction of highly active antiretroviral therapy (1996 onwards). Our data show that in addition to the influx of HCV-4 strains from countries where HCV-4 is endemic, the local spread of HCV-4d affecting injecting drug users and, in recent years, especially HIV-positive MSM will further increase the relative proportion of HCV-4-infected patients in The Netherlands. HCV-4-specific agents are drastically needed to improve treatment response rates and decrease the future burden of HCV-4-related disease.

New Strain of Salmonella

Antibiotic resistant bacteria have become a worldwide public health issue. Researchers have identified a new strain of Salmonella typhimurium, called ST313, that has become more virulent among people living in sub-Saharan Africa regions.

The bacteria have undergone genetic changes that have allowed them to not only become resistant to commonly used antibiotics, but they are also less responsive to drugs in which they have not gained resistance. Researcher Dr. Chisomo Msefula states, "Our findings show that ST313 has acquired a block of genes that make it resistant to the common antibiotics. The genes jumped into ST313 on a mobile genetic element called a transposon, bringing with it additional genes that make the strain more deadly." The researchers hope that insight gained from this study can be used to develop new vaccines to fight against these and similar pathogens.