Orphan Genes Shared by Pathogenic Genomes Are More Associated with Bacterial Pathogenicity

Orphan genes (also known as ORFans [i.e., orphan open reading frames]) are new genes that enable an organism to adapt to its specific living environment. Our focus in this study is to compare ORFans between pathogens (P) and nonpathogens (NP) of the same genus. Using the pangenome idea, we have identified 130,169 ORFans in nine bacterial genera (505 genomes) and classified these ORFans into four groups: (i) SS-ORFans (P), which are only found in a single pathogenic genome; (ii) SS-ORFans (NP), which are only found in a single nonpathogenic genome; (iii) PS-ORFans (P), which are found in multiple pathogenic genomes; and (iv) NS-ORFans (NP), which are found in multiple nonpathogenic genomes. Within the same genus, pathogens do not always have more genes, more ORFans, or more pathogenicity-related genes (PRGs)—including prophages, pathogenicity islands (PAIs), virulence factors (VFs), and horizontal gene transfers (HGTs)—than nonpathogens. Interestingly, in pathogens of the nine genera, the percentages of PS-ORFans are consistently higher than those of SS-ORFans, which is not true in nonpathogens. Similarly, in pathogens of the nine genera, the percentages of PS-ORFans matching the four types of PRGs are also always higher than those of SS-ORFans, but this is not true in nonpathogens. All of these findings suggest the greater importance of PS-ORFans for bacterial pathogenicity

Identification and investigation of ORFans in the viral world

<p>Abstract</p> <p>Background</p> <p>Genome-wide studies have already shed light into the evolution and enormous diversity of the viral world. Nevertheless, one of the unresolved mysteries in comparative genomics today is the abundance of ORFans – ORFs with no detectable sequence similarity to any other ORF in the databases. Recently, studies attempting to understand the origin and functions of bacterial ORFans have been reported. Here we present a first genome-wide identification and analysis of ORFans in the viral world, with focus on bacteriophages.</p> <p>Results</p> <p>Almost one-third of all ORFs in 1,456 complete virus genomes correspond to ORFans, a figure significantly larger than that observed in prokaryotes. Like prokaryotic ORFans, viral ORFans are shorter and have a lower GC content than non-ORFans. Nevertheless, a statistically significant lower GC content is found only on a minority of viruses. By focusing on phages, we find that 38.4% of phage ORFs have no homologs in other phages, and 30.1% have no homologs neither in the viral nor in the prokaryotic world. Phages with different host ranges have different percentages of ORFans, reflecting different sampling status and suggesting various diversities. Similarity searches of the phage ORFeome (ORFans and non-ORFans) against prokaryotic genomes shows that almost half of the phage ORFs have prokaryotic homologs, suggesting the major role that horizontal transfer plays in bacterial evolution. Surprisingly, the percentage of phage ORFans with prokaryotic homologs is only 18.7%. This suggests that phage ORFans play a lesser role in horizontal transfer to prokaryotes, but may be among the major players contributing to the vast phage diversity.</p> <p>Conclusion</p> <p>Although the current sampling of viral genomes is extremely low, ORFans and near-ORFans are likely to continue to grow in number as more genomes are sequenced. The abundance of phage ORFans may be partially due to the expected vast viral diversity, and may be instrumental in understanding viral evolution. The functions, origins and fates of the majority of viral ORFans remain a mystery. Further computational and experimental studies are likely to shed light on the mechanisms that have given rise to so many bacterial and viral ORFans.</p

Open reading frames provide a rich pool of potential natural antisense transcripts in fungal genomes

Natural antisense transcripts are reported from all kingdoms of life and several recent reports of genomewide screens indicate that they are widely distributed. These transcripts seem to be involved in various biological functions and may govern the expression of their respective sense partner. Very little, however, is known about the degree of evolutionary conservation of antisense transcripts. Furthermore, none of the earlier analyses has studied whether antisense relationships are solely dual or involved in more complex relationships. Here we present a systematic screen for cis- and trans-located antisense transcripts based on open reading frames (ORFs) from five fungal species. The relative number of ORFs involved in antisense relationships varies greatly between the five species. In addition, other significant differences are found between the species, such as the mean length of the antisense region. The majority of trans-located antisense transcripts is found to be involved in complex relationships, resulting in highly connected networks. The analysis of the degree of evolutionary conservation of antisense transcripts shows that most antisense transcripts have no ortholog in any other species. An annotation of antisense transcripts based on Gene Ontology directs to common terms and shows that proteins of genes involved in antisense relationships preferentially localize to the nucleus with common functions in the regulation or maintenance of nucleic acids

Powerful sequence similarity search methods and in-depth manual analyses can identify remote homologs in many apparently "orphan" viral proteins.

The genome sequences of new viruses often contain many "orphan" or "taxon-specific" proteins apparently lacking homologs. However, because viral proteins evolve very fast, commonly used sequence similarity detection methods such as BLAST may overlook homologs. We analyzed a data set of proteins from RNA viruses characterized as "genus specific" by BLAST. More powerful methods developed recently, such as HHblits or HHpred (available through web-based, user-friendly interfaces), could detect distant homologs of a quarter of these proteins, suggesting that these methods should be used to annotate viral genomes. In-depth manual analyses of a subset of the remaining sequences, guided by contextual information such as taxonomy, gene order, or domain cooccurrence, identified distant homologs of another third. Thus, a combination of powerful automated methods and manual analyses can uncover distant homologs of many proteins thought to be orphans. We expect these methodological results to be also applicable to cellular organisms, since they generally evolve much more slowly than RNA viruses. As an application, we reanalyzed the genome of a bee pathogen, Chronic bee paralysis virus (CBPV). We could identify homologs of most of its proteins thought to be orphans; in each case, identifying homologs provided functional clues. We discovered that CBPV encodes a domain homologous to the Alphavirus methyltransferase-guanylyltransferase; a putative membrane protein, SP24, with homologs in unrelated insect viruses and insect-transmitted plant viruses having different morphologies (cileviruses, higreviruses, blunerviruses, negeviruses); and a putative virion glycoprotein, ORF2, also found in negeviruses. SP24 and ORF2 are probably major structural components of the virions