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7.11F: Gene Transfer in Archaea - Biology

7.11F: Gene Transfer in Archaea - Biology



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Archaea are distinct from bacteria and eukaryotes, but genetic material can be transferred between them and between Archaea themselves.

LEARNING OBJECTIVES

Describe the mechanisms of gene transfer in Archaea

Key Takeaways

Key Points

  • Archaea while being very different from eukaryotes and bacteria, there are many commonalities at the the genetic level between them.
  • Horizontal gene transfer can explain the similarities between the genes found in the three domains of life and indeed there is evidence that horizontal gene transfer occurs with Archaea species.
  • Archaea can be infected by double-stranded DNA viruses, which can account for gene transfers, as well like bacteria, Archaea may conjugate.

Key Terms

  • archaea: a taxonomic domain of single-celled organisms lacking nuclei that are fundamentally from bacteria.
  • translation: Translation is the communication of the meaning of a source-language text by means of an equivalent target-language text.
  • transcription: Transcription is the process of creating a complementary RNA copy of a sequence of DNA. Both RNA and DNA are nucleic acids, which use base pairs of nucleotides as a complementary language that can be converted back and forth from DNA to RNA by the action of the correct enzymes.

Archaea are genetically distinct from bacteria and eukaryotes, but are poorly understood: many of the genes that Archaea encode are of unknown function. Transcription and translation in archaea resemble the same processes more closely in eukaryotes than in bacteria, with the archaean RNA polymerase and ribosomes being very close to their equivalents in eukaryotes.

Although Archaea only have one type of RNA polymerase, its structure and function in transcription is similar to that of the eukaryotic RNA polymerase II, with similar protein assemblies (the general transcription factors) directing the binding of the RNA polymerase to a gene’s promoter. However, other archaean transcription factors are closer to those found in bacteria. Post-transcriptional modification is simpler than in eukaryotes, since most archaean genes lack introns, although there are many introns in their transfer RNA and ribosomal RNA genes, and introns may occur in a few protein-encoding genes. This is all to say there are many similarities in the genes shared between Archaea and the other domains of life, suggesting there was a transfer of genetic material between the domains of life. This phenomenon is described as horizontal gene transfer.

Horizontal gene transfer (HGT) refers to the transfer of genes between organisms in a manner other than traditional reproduction. Also termed lateral gene transfer, it contrasts with vertical transfer, the transmission of genes from the parental generation to offspring via sexual or asexual reproduction. HGT has been shown to be an important factor in the evolution of many organisms, including bacteria, plants and humans.

Archaea show high levels of horizontal gene transfer between lineages. Some researchers suggest that individuals can be grouped into species-like populations given highly similar genomes and infrequent gene transfer to/from cells with less-related genomes, as in the Archaea genus Ferroplasma. On the other hand, studies in Halorubrum found significant genetic transfer to/from less-related populations. These gene transfers are identified by sequencing the DNA of various Archaea species; through the similarities and differences of the DNA of the different types of Archaea it is determined if the gene was perfectly transferred or from a common ancestor. The elucidation of this can be controversial.

How genetic material can move from one Archaea to another is poorly understood. In bacteria the natural ways in which this occurs is through either bacterial conjugation or viral transfer, also known as transduction. Conjugation is where two (sometimes distantly related) bacteria transfer genetic material by direct contact. Transduction occurs when a virus “picks up” some DNA from its host and when infecting a new host, moves that genetic material to the new host. It is thought that conjugation can occur in Archaea, though unlike bacteria the mechanism is not well understood. As well Archaea can be infected by viruses. In fact Archaea can be infected by double-stranded DNA viruses that are unrelated to any other form of virus and have a variety of unusual shapes, including bottles, hooked rods, or teardrops. Taken together it is clear that gene transfer happens in Archaea, and probably is similar to horizontal gene transfer seen in the other domains of life.


Assessing the benefits of horizontal gene transfer by laboratory evolution and genome sequencing

Recombination is widespread across the tree of life, because it helps purge deleterious mutations and creates novel adaptive traits. In prokaryotes, it often takes the form of horizontal gene transfer from a donor to a recipient bacterium. While such transfer is widespread in natural communities, its immediate fitness benefits are usually unknown. We asked whether any such benefits depend on the environment, and on the identity of donor and recipient strains. To this end, we adapted Escherichia coli to two novel carbon sources over several hundred generations of laboratory evolution, exposing evolving populations to various DNA donors.

Results

At the end of these experiments, we measured fitness and sequenced the genomes of 65 clones from 34 replicate populations to study the genetic changes associated with adaptive evolution. Furthermore, we identified candidate de novo beneficial mutations. During adaptive evolution on the first carbon source, 4-Hydroxyphenylacetic acid (HPA), recombining populations adapted better, which was likely mediated by acquiring the hpa operon from the donor. In contrast, recombining populations did not adapt better to the second carbon source, butyric acid, even though they suffered fewer extinctions than non-recombining populations. The amount of DNA transferred, but not its benefit, strongly depended on the donor-recipient strain combination.

Conclusions

To our knowledge, our study is the first to investigate the genomic consequences of prokaryotic recombination and horizontal gene transfer during laboratory evolution. It shows that the benefits of recombination strongly depend on the environment and the foreign DNA donor.


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Vol 339, Issue 6124
08 March 2013

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By Gerald Schönknecht , Wei-Hua Chen , Chad M. Ternes , Guillaume G. Barbier , Roshan P. Shrestha , Mario Stanke , Andrea Bräutigam , Brett J. Baker , Jillian F. Banfield , R. Michael Garavito , Kevin Carr , Curtis Wilkerson , Stefan A. Rensing , David Gagneul , Nicholas E. Dickenson , Christine Oesterhelt , Martin J. Lercher , Andreas P. M. Weber

Science 08 Mar 2013 : 1207-1210

A mosaic of genes acquired from various phyla enable a red alga to grow abundantly in hot, acidic, and toxic niches. [Also see Perspective by Rocha]


INTRA- AND INTERSPECIFIC GENETIC EXCHANGE

Better than Sex

In sexual eukaryotes, the theoretical advantages of genetic exchange, through the elimination of deleterious mutations and the combination of favorable ones, are well established. Horizontal gene transfer provides the same advantages when the acquisition of DNA is from conspecifics, although recombination is not associated with reproduction. However, these movements of genetic information extend well beyond the species boundaries. Many cases of horizontal transfers have been described, particularly in connection with the acquisition of new functions and colonization of new ecological niches. In particular, the capacity shown by some bacterial strains of acquiring virulence genes or antibiotic resistance remains a major health problem. Yet, one can wonder whether these cases are anecdotal, or if, instead, the horizontal transfer is a mechanism that plays a key role in the evolution of prokaryotes. Answering this question involves detecting transfers between species, to quantify their importance.

The Many Facets of Horizontal Transfer

There are three major types of approaches to identifying horizontal transfers in completely sequenced genomes:

Methods for comparison of gene repertoires contrast genomes of related species or strains of the same species and often reveal very different gene content. These differences in gene repertoires are explained by gene losses (deletions) and/or gains. However, as in the case of Escherichia coli, bacterial strains of the same species frequently have hundreds of genes that are strain specific. In such cases, we must either assume an ancestral genome of astronomical size, to interpret these differences by genes losses, or accept that differences between closely related strains are mostly the result of recent integrations (Daubin et al. 2003a Touchon et al. 2009).

Methods of gene composition analysis rely on the long-standing observation that there is a great diversity of G+C content among bacterial genomes (Sueoka 1962) and that each genome has a base composition and codon usage that can be diagnostic of the species. However, regions having contrasting nucleotide or codon composition are often found in bacterial genomes. This suggests that such regions originate from recent transfer from genomes having different compositions (Lawrence and Ochman 1998 Ochman et al. 2000). As relatively closely related organisms (such as enterobacteriaceae, for example) have comparable G+C content, genes with diverging G+C content are generally considered as originating from more distant organisms. Overall, these methods are expected to underestimate the number of transfers, for two reasons. First, they are not able to identify transfers from species having a composition similar to the host genome. Second, these methods cannot find ancient transfers, because these genes, once integrated, gradually acquire the characteristics of the host genome. It is worth noting, although, that some mechanisms probably maintain an heterogeneity of G+C content of genes within bacterial genomes, which could be deceiving for these methods (Guindon and Perrière 2001 Daubin and Perrière 2003 Lassalle et al. 2015).

Phylogenetic methods are the most general, and potentially most sensitive, methods for inferring horizontal transfers. These methods reconstruct the history of a family of homologous genes (a gene tree), and compare it to a putative history of the species in which the genes are found (the species tree). Phylogenetically well-supported disagreements between the two trees can be interpreted in terms of transfers. Such methods have the advantage of providing information on the donor species (not just the recipient) and can, in theory, identify ancient transfers. The difficulty of this approach is that it requires a reference phylogeny, and the ability to differentiate between different types of events that can change the history of a gene such as duplications, losses, and transfers (see Fig. 1 ). Most studies aimed at evaluating the role of gene transfer using phylogenetic approaches have tried to circumvent the problem of duplications and loss of genes by focusing on genes that are present in at most one copy in each genome (Beiko et al. 2005 Than et al. 2008 Abby et al. 2010, 2012 Puigbò et al. 2010). Only recently, new methods have been developed that can sort out the role of duplication, transfer, and loss in gene histories (Bansal et al. 2012 Szöllősi et al. 2012, 2013b Sjöstrand et al. 2014). A crucial ingredient of any phylogenetic method that aims at detecting gene transfer is the ability to account for phylogenetic uncertainty. Taking into consideration phylogenetic uncertainty is important, because limited signal leads to reconstruction errors that subsequently result in a gross overestimate of the amount of horizontal gene transfer. To overcome this problem, it is possible to exploit the fact that, although each homologous gene family has its own unique story, they are all related by a shared species history, and this history can be helpful for gene tree inference. In a study that attempted to take into account shared species history for gene tree reconstruction in cyanobacteria (Szöllősi et al. 2013a), the majority of phylogenetic discord was found to result from reconstruction errors. This can be corrected by combining information from sequence alignment with information from a putative species tree and probabilities of duplication, transfer, and loss optimized across gene families. The result is a striking reduction in apparent phylogenetic discord, with 24%, 59%, and 46% reductions, respectively, in the mean numbers of duplications, transfers, and losses per gene family.

The processes of discord. Three biological processes can generate gene trees that differ from the species tree. (A) The combined action of gene duplication and loss, (B) horizontal gene transfer, and (C) deep coalescence, where polymorphic alleles can remain present in a population for a time than spans two speciations (black squares show the alleles that coexist for this period). In each of these examples, the genes from species C and D are closest relatives, although species C is more closely related to species B (adapted from Maddison 1997).

More generally, the three approaches described above give seemingly very different ideas about the impact of horizontal transfer on genomes (Ragan 2001 Lawrence and Ochman 2002). The first two show that genomes can contain high proportions of 𠇏oreign” genes, up to 20%, acquired recently. The third approach, in contrast, has limited power to detect very recent transfers, but phylogenetic incongruities are clearly evident when studying the genomes of distant species (Daubin et al. 2003b). This apparent contradiction between the different approaches can, in fact, be interpreted as a fundamental underlying difference in the time scale considered. An individual genome sequence corresponds to the shortest time scale. It is a snapshot of the genetic information of a species (or strain) at a particular instance in time. Such a genomic snapshot can contain hundreds of recently acquired genes, the overwhelming majority of which are destined to disappear in the short term, leaving little trace in gene phylogenies (Daubin et al. 2003b Lerat et al. 2005). Analysis of recently acquired genes shows that the vast majority are orphans, or “ORFans” (i.e., genes that have no homologs in the other known genomes) (Siew and Fischer 2003). One possible explanation is that these genes originate from bacteriophages that have integrated into the genome. To be retained in the longer term, they would have to turn out to be useful for their host (Daubin et al. 2003a Daubin and Ochman 2004a,b Cortez et al. 2009 Bobay et al. 2014).

Horizontal Transfer and Adaptation

The adaptive role of horizontal transfer in bacteria is well established. In particular, there are long stretches of genomes called “islands” that are only present sporadically in a given species, and are associated with pathogenicity, symbiosis with another organism (e.g., a plant), or other ecological characteristics (Dobrindt et al. 2004). The grouping of these genes in islands is probably a result of the fact that these genes are associated with mobile elements (transposons, bacteriophages) that tend to recombine with each other and thus are inserted in close proximity to each other, which then promotes their simultaneous transfer from one genome to another. Interestingly, these islands usually contain numerous “ORFans” whose function, if they have one, has not yet been discovered (Siew and Fischer 2003).

These examples are evidence for the existence of recent horizontal transfer in conjunction with immediate environmental benefits, but there are also many indications suggesting that ancient transfers have been able to touch even the most fundamental cellular function. One example is the case of reverse gyrase, a protein that changes the conformation of the chromosome, is found in all hyperthermophilic and some thermophilic organisms (Bacteria and Archaea) and is thought to have been acquired repeatedly to adapt to this unique environment (Brochier-Armanet and Forterre 2006). Also, many examples of transfers of genes encoding tRNA synthetases, whose function is to load the amino acids onto their tRNAs before translation, have been described between phylogenetically distant organisms (Fournier et al. 2015). The selection pressures that promote such transfers are still poorly understood, but it is possible that these enzymes, which generally operate without interacting with other proteins, and whose substrates (an amino acid and tRNA) are highly conserved in evolution and can hence adapt relatively easily to a new cellular environment. This type of reasoning is consistent with the “hypothesis of complexity” (Jain et al. 1999), which maintains that the number of molecular interactions of the protein encoded by a gene is a barrier to transfer. For example, genes involved in complex molecular structures, such as ribosomes or DNA replication machinery, are considered less likely to be replaced by remote homologs, because they have a low probability of having preserved their numerous sites of interactions intact. However, there are exceptions to this rule, and, specifically, certain ribosomal genes show clear traces of horizontal transfer (Brochier et al. 2000).


Thane Papke Wins NASA Grant to Study Gene Transfer in Archaea

Human evolution is based on the premise of “survival of the fittest” where the organisms with the genetically encoded characteristics best suited to their environment survive to pass those genes on to their offspring who keep passing that trait on until all members of the population have it. But how do organisms that don’t reproduce sexually evolve?

Archaea are a type of single-celled organism that can be found all over the globe, often in extreme environments. They help make up sea plankton which are the basis of all marine food chains, some live in hot springs and salt lakes, some even reside in the human gut and play an important role in digestion. But how this class of organisms, which may be the oldest on the planet, has evolved over billions of years largely remains a mystery.

The work of University of Connecticut associate professor of molecular and cell biology R. Thane Papke may help illuminate part of this mystery. Papke has received a $989,000 grant from the National Aeronautics and Space Administration to study the role of horizontal gene transfer in archaeal evolution. Simon White, also from UConn, is a co-investigator, and Uri Gophna from Tel-Aviv University in Israel is an international co-investigator for this grant.

Archaea and bacteria reproduce asexually. These organisms copy their DNA and make a perfect replica of themselves. This is why horizontal gene transfer is essential for the evolution of these organisms which otherwise would have no way to diversify their allele pool and ensure the survival of the species. If all members of a species have the same genetic profile, a single disease can wipe all members of that species out in one fell swoop.

Studies have shown archaea engage in a tremendous amount of horizontal gene transfer (HGT) and that they have acquired thousands of genes from bacterial sources. This has resulted in non-sexually reproducing organisms having the same amount of genetic diversity as sexually producing organisms, leaving evolutionary researchers scratching their heads.

“Sexual reproduction is thought to have arisen out of asexuality precisely because of the advantages of shuffling gene pools,” Papke says. “However, it is clear that archaea and bacteria had solved that problem without sexual reproduction.”

Previous studies have shown evidence of a cell-contact-dependent method of gene transfer in a type of archaea called H. volcanii, which is commonly found in the Dead Sea and other very salty environments.

Haloarchaea engage in a kind of horizontal gene transfer known as “mating” wherein two archaea swap genes through cell-to-cell contact without a clear donor/recipient dynamic which is seen in most other forms of HGT.

This archaeon’s ability to survive in such environments makes it attractive to space researchers as these organisms could potentially live on Mars and offer insight into the evolution of extraterrestrial life there.

“I think NASA funds our work because we address fundamental questions that attempt to resolve where sexual reproduction comes from,” Papke says. “NASA is interested in transitional states of biology, and sexual reproduction is a big one.”

In this project, Papke hopes to identify and characterize the genes responsible for horizontal gene transfer in this particular archaeon. Papke and his team also hope to determine the rate of horizontal gene transfer between haloarchaeal species, the class to which H. volcanii belongs.

Papke will also study the role of the receiving organism’s system for cutting non-self DNA in this process, which is how cells can be immune from virus or plasmid infection. Whenever organisms encounter foreign material, their immune systems naturally react and attempt to remove or destroy the invader. For a cell to take up a foreign gene successfully, its immune system must be overridden and signaled to stand down.

One of the features that makes H. volcanii an ideal model organism for this research because their method of horizontal gene transfer requires the membranes and cell walls of two or more cells to fuse, in a way that interestingly resembles the fusion of gametes to produce a zygote through sexual reproduction.

“This resembles what I would imagine as a primitive intermediate step towards sexual reproduction that demonstrates an expected cell contact mechanism for wholesale genetic flow, without having connected reproduction to the process yet, a kind of asexual reproduction sex,” Papke says.


Gene Transfer in Archaea

Archaea are distinct from bacteria and eukaryotes, but genetic material can be transferred between them and between Archaea themselves.

Learning Objectives

Describe the mechanisms of gene transfer in Archaea

Key Takeaways

Key Points

  • Archaea while being very different from eukaryotes and bacteria, there are many commonalities at the the genetic level between them.
  • Horizontal gene transfer can explain the similarities between the genes found in the three domains of life and indeed there is evidence that horizontal gene transfer occurs with Archaea species.
  • Archaea can be infected by double-stranded DNA viruses, which can account for gene transfers, as well like bacteria, Archaea may conjugate.

Key Terms

  • archaea: a taxonomic domain of single-celled organisms lacking nuclei that are fundamentally from bacteria.
  • translation: Translation is the communication of the meaning of a source-language text by means of an equivalent target-language text.
  • transcription: Transcription is the process of creating a complementary RNA copy of a sequence of DNA. Both RNA and DNA are nucleic acids, which use base pairs of nucleotides as a complementary language that can be converted back and forth from DNA to RNA by the action of the correct enzymes.

Archaea are genetically distinct from bacteria and eukaryotes, but are poorly understood: many of the genes that Archaea encode are of unknown function. Transcription and translation in archaea resemble the same processes more closely in eukaryotes than in bacteria, with the archaean RNA polymerase and ribosomes being very close to their equivalents in eukaryotes.

Although Archaea only have one type of RNA polymerase, its structure and function in transcription is similar to that of the eukaryotic RNA polymerase II, with similar protein assemblies (the general transcription factors) directing the binding of the RNA polymerase to a gene’s promoter. However, other archaean transcription factors are closer to those found in bacteria. Post-transcriptional modification is simpler than in eukaryotes, since most archaean genes lack introns, although there are many introns in their transfer RNA and ribosomal RNA genes, and introns may occur in a few protein-encoding genes. This is all to say there are many similarities in the genes shared between Archaea and the other domains of life, suggesting there was a transfer of genetic material between the domains of life. This phenomenon is described as horizontal gene transfer.

Horizontal gene transfer (HGT) refers to the transfer of genes between organisms in a manner other than traditional reproduction. Also termed lateral gene transfer, it contrasts with vertical transfer, the transmission of genes from the parental generation to offspring via sexual or asexual reproduction. HGT has been shown to be an important factor in the evolution of many organisms, including bacteria, plants and humans.

Archaea show high levels of horizontal gene transfer between lineages. Some researchers suggest that individuals can be grouped into species-like populations given highly similar genomes and infrequent gene transfer to/from cells with less-related genomes, as in the Archaea genus Ferroplasma. On the other hand, studies in Halorubrum found significant genetic transfer to/from less-related populations. These gene transfers are identified by sequencing the DNA of various Archaea species through the similarities and differences of the DNA of the different types of Archaea it is determined if the gene was perfectly transferred or from a common ancestor. The elucidation of this can be controversial.

How genetic material can move from one Archaea to another is poorly understood. In bacteria the natural ways in which this occurs is through either bacterial conjugation or viral transfer, also known as transduction. Conjugation is where two (sometimes distantly related) bacteria transfer genetic material by direct contact. Transduction occurs when a virus “picks up” some DNA from its host and when infecting a new host, moves that genetic material to the new host. It is thought that conjugation can occur in Archaea, though unlike bacteria the mechanism is not well understood. As well Archaea can be infected by viruses. In fact Archaea can be infected by double-stranded DNA viruses that are unrelated to any other form of virus and have a variety of unusual shapes, including bottles, hooked rods, or teardrops. Taken together it is clear that gene transfer happens in Archaea, and probably is similar to horizontal gene transfer seen in the other domains of life.

Archaeal viral infection: Cell of Sulfolobus infected by virus STSV1 observed under microscopy. Two spindle-shaped viruses were being released from the host cell. The strain of Sulfolobus and STSV1 (Sulfolobus tengchongensis Spindle-shaped Virus 1) were isolated by Xiaoyu Xiang and his colleagues in an acidic hot spring in Yunnan Province, China. At present, STSV1 is the largest archaeal virus to have been isolated and studied. Its genome sequence has been sequenced.


Fundamentals of Molecular Evolution*

Supratim Choudhuri , in Bioinformatics for Beginners , 2014

2.3.4.1.D Horizontal Gene Transfer

Horizontal gene transfer , also known as lateral gene transfer, refers to nonsexual transmission of genetic material between unrelated genomes hence, horizontal gene transfer involves gene transfer across species boundaries. The phenomenon of horizontal gene transfer throws a wrench in the concepts of last common ancestor, syntenic relationship between genomes, phylogeny and the evolution of discrete species units, taxonomic nomenclature, etc. m The majority of examples of horizontal gene transfer are known in prokaryotes. In bacteria, three principal mechanisms can mediate horizontal gene transfer: transformation (uptake of free DNA), conjugation (plasmid-mediated transfer), and transduction (phage-mediated transfer). In plants, introgression can mediate horizontal gene transfer this means gene flow from one gene pool to another gene pool—that is, from one species to another species by repeated backcrossing between an interspecific hybrid and one of its parent species. Therefore, introgression depends on the extent of reproductive isolation between the two species. Introgression has also been reported between duck species, between butterfly species involved in mimicry, and between human and Neanderthal. 41

Horizontal gene transfer in animals is not common, but there are some reports. For example, Acuña et al. 42 identified the gene HhMAN1 from the coffee berry borer beetle, Hypothenemus hampei, which shows clear evidence of horizontal gene transfer from bacteria. HhMAN1 encodes the enzyme mannanase, which hydrolyzes galactomannan. Phylogenetic analyses of the mannanase from both prokaryotes and eukaryotes revealed that mannanases from plants, fungi, and animals formed a distinct eukaryotic clade, but HhMAN1 was most closely related to prokaryotic mannanases, grouping with the Bacillus clade. HhMAN1 was not detected in the closely related species H. obscurus, which does not colonize coffee beans. The authors hypothesized that the acquisition of the HhMAN1 gene from bacteria was likely an adaptation in response to need in a specific ecological niche.

There are also some examples of horizontal gene transfer from fungi to arthropods, such as aphids (insects) and mites (arachnids). Phylogenetic analysis revealed the evidence of horizontal transfer of genes encoding carotenoid desaturase and carotenoid cyclase–carotenoid synthase from fungi to pea aphid, 43 and to spider mite. 44 Notably, the fused carotenoid cyclase–carotenoid synthase gene is characteristic of fungi but not of plants or bacteria. The authors discussed the possible mechanism of such gene transfer. Gene transfer into a single arthropod ancestor of both spider mites and aphids is not likely because it would require subsequent loss of these genes in most other living arthropod taxa. The most likely scenario is the transfer of these genes through symbiosis, which probably occurred independently in both aphids and spider mites. It has been suggested that the frequent association of mites with viruses makes them ideal horizontal gene transfer vectors, including incorporation of mobile genes into their own genomes.


Gene transfer agents: phage-like elements of genetic exchange

Horizontal gene transfer is important in the evolution of bacterial and archaeal genomes. An interesting genetic exchange process is carried out by diverse phage-like gene transfer agents (GTAs) that are found in a wide range of prokaryotes. Although GTAs resemble phages, they lack the hallmark capabilities that define typical phages, and they package random pieces of the producing cell's genome. In this Review, we discuss the defining characteristics of the GTAs that have been identified to date, along with potential functions for these agents and the possible evolutionary forces that act on the genes involved in their production.

Conflict of interest statement

Competing interests statement

The authors declare no competing financial interests.

Figures

Figure 1. Comparison of gene transfer agent…

Figure 1. Comparison of gene transfer agent and transducing phage production

Figure 2. Electron micrographs of gene transfer…

Figure 2. Electron micrographs of gene transfer agent particles

The estimated sizes of the particles…

Figure 3. Gene transfer agent-encoding gene clusters

Figure 3. Gene transfer agent-encoding gene clusters

The general organizations of genes encoding the two…

Figure 4. Distribution of gene transfer agent…

Figure 4. Distribution of gene transfer agent genes in alphaproteobacteria and spirochaetes

Figure 5. Evidence of purifying selection in…

Figure 5. Evidence of purifying selection in selected gene transfer agent genes in the Rhodobacterale…


Background

The appearance of land plants was a key step towards the development of modern terrestrial ecosystems. Fossil data indicate that the first land plants appeared around 500 million years ago, from a pioneer green algal ancestor probably related to Charales [1, 2].

Early terrestrial environments were harsh. The ancestor of land plants that conquered emerged lands had to face important stresses including desiccation, UV radiation (not anymore shielded by water), as well as attack by already diversified microbial soil communities [1, 3]. This drove a number of key adaptations, including the emergence of specialized secondary metabolic pathways. Among them, the phenylpropanoid pathway was crucial. It is in fact a ubiquitous and specific trait of land plants, and provides vital compounds such as lignin -essential for vascularization (xylem) and stem rigidity out of water-, and flavonoids -essential for reproductive biology (flower and fruit colors), protection against UV (pigments) and microbial attack (phytoalexins), and plant-microbe interaction (flavonoids) [4, 5]. Three steps constituting the general phenylpropanoid pathway provide the precursors for the flavonoid and lignin branches (Figure 1). Phenylalanine ammonia-lyase (PAL) transforms phenylalanine into trans-cinnamic acid, which leads to p-coumaric acid by the action of cinnamic acid 4-hydrolase (CH4), which is then transformed into p-coumaroyl-CoA by p-coumaroyl:CoA ligase (4CL) (Figure 1). Either p-coumaric acid and p-coumaroyl-CoA can enter the lignin monomer pathway, while p-coumaroyl-CoA is the precursor of the flavonoid pathway (Figure 1). Lignin monomer and flavonoid biosynthesis then involve complex highly branched pathways (Figure 1)[4, 6].

A schematic representation of phenylpropanoid metabolism. From the general phenylpropanoid pathway (top left, reactions from L-phenylalanine to p-Coumaroyl-CoA) two separated branches lead to the production of lignin monomers (right) and of flavonoids (bottom). Solid arrows indicate a single step enzymatic reaction, dashed arrows multiple sequential enzymatic reactions. Enzymes are reported with a three letter code: PAL, phenylalanine ammonia lyase TAL, tyrosine ammonia lyase C4H, cinnamate 4-hydroxylase 4CL, 4-coumarate CoA ligase COMT, caffeic acid/5-hydroxyferulic acid O-methyltransferase HCT/CST, hydroxycinnamoyl CoA:shikimate/quinate hydroxycinnamoyltransferase C3H, p-coumaroyl shikimate/quinate 3-hydroxylase CCoAOMT, caffeoyl CoA O-methyltransferase CCR, (hydroxy)cinnamoyl CoA reductase CAD, (hydroxy)cinnamyl alcohol dehydrogenase F5H ferulate 5-hydroxylase CHS, chalcone synthase STS, stilbene synthase.

The initial physiological advantage of phenolic compounds is not clear. In fact, flavonoids are not thought to have been immediately effective as UV protection before the emergence of complex structures allowing for their accumulation in large quantities, and it has been proposed that they were initially used as internal signaling molecules [7]. Lignin-like polymers have been identified in the cell walls of the charalean alga Nitella and in bryophytes (mosses, liverworts, and hornworts), early branching lineages of land plants that do not harbor a developed vascular system such as that found in Tracheophytes (Ferns, Gymnosperms and Angiosperms) [8]. Because these lignin monomers in non vascular plants do not fulfill structural functions it has been proposed that may principally serve as a defense mechanism against microorganisms or UV radiation [8]. To date, there is no evidence for the presence of a full phenylpropanoid metabolism in organisms other than land plants, although some bacteria and fungi harbor homologues of a few enzymes of the pathway [9, 10].

The phenylpropanoid pathway likely evolved progressively in land plants by the recruitment of enzymes from the primary metabolism (for a recent review see 4). However, the origin of PAL was a key event, since it provided the initial step from which the rest of the pathway was assembled. Indeed, PAL is a key regulator of the phenylpropanoid pathway [11] and any inhibition of PAL blocks the whole pathway. Probably due to its essentiality, land plants harbor multiple copies of PAL [5] and no complete null mutant is available in the literature. De novo synthesis of PAL is induced in response to different stress stimuli such as UV irradiation, pathogenic attack, low levels of nitrogen, phosphate, or iron [6]. Although PAL enzymes have been extensively characterized in all land plants lineages, including the early emerging bryophytes (mosses, liverworts, and hornworts), their distribution in other organisms is limited. PAL are known to be present in fungi, in particular Basidiomicetes yeasts such as Rhodotorula, but also Ascomycetes such as Aspergillus and Neurospora, where they participate to the catabolism of phenylalanine as a source of carbon and nitrogen [12–14].

The PAL of some plants and fungi also harbor a tyrosine ammonia lyase (TAL) activity that is responsible for the synthesis of p-coumaric acid directly from tyrosine, which in turn leads to the production of p-coumaroyl-CoA [4] (Figure 1). PAL enzymes have been functionally characterized from a few sediment/soil bacteria such as Streptomyces maritimus (Actinobacteria), where PAL is required to supply cinnamic acid for the production of benzoyl-CoA, the starter molecule for the biosynthesis of the bacteriostatic agent enterocin [15], and Photorhabdus luminescens (γ-Proteobacteria), where PAL is essential for the production of the powerful stilbene antibiotic through yet unknown intermediate steps [16, 17]. More recently, PAL have also been identified and structurally characterized in two Cyanobacteria belonging to the order Nostocales, where they are involved in a pathway whose end product is yet unknown [18]. From functional studies, it has been proposed that these cyanobacterial PAL might represent an evolutionary intermediate towards plants PAL [18]. PAL homologues with TAL activity have also been identified in some bacteria such as the Actinobacterium Saccharotrix espanaensis, where they are used to produce the antibiotic saccharomicin [19], and in purple phototrophic a-Proteobacteria such as Rhodobacter, where they are involved in the synthesis of the chromophore of their photoactive yellow protein photoreceptor [20].

PAL is homologous to histidine ammonia lyase (HAL), which is involved in the catabolism of histidine and is widespread in prokaryotes and eukaryotes [21, 22]. It has been proposed that "PAL developed from HAL when fungi and plants diverged from the other kingdoms" [4]. However, the current view of eukaryotic evolution based on phylogenetic analyses indicates that fungi and plants do not share an exclusive ancestor [23, 24]. In fact, Fungi are more related to Animals than to land plants. Moreover, land plants belong to the phylum Plantae, which also includes Glaucocystophytes, red algae, and green algae [23, 24].

Given the clear importance of PAL in the emergence of the phenylpropanoid pathway and adaptation of plants to land, we sought to get more insight into the origin of this enzyme by carrying out an extensive search of PAL/TAL/HAL homologues in current sequence databases and by analyzing their phylogeny.


New Genes = New Archaea?

Molly Sharlach
Oct 15, 2014

Carotenoid-producing haloarchaea impart a red color to salt ponds in San Francisco Bay. WIKIMEDIA, GROMBO

While mutation and sexual reproduction drive genetic innovation in many eukaryotes, for life&rsquos exclusively unicellular domains&mdasharchaea and bacteria&mdashhorizontal gene transfer is a critical mechanism for gaining new traits. And genes acquired from bacteria appear to have played an important role in forming major taxa of archaea, according to a phylogenetic analysis of more than 25,000 archaeal gene families. The study, published today (October 15) in Nature, also suggests that genetic transfers from bacteria to archaea are at least five times more common than from archaea to bacteria.

&ldquoWe tend to think of evolution as proceeding in a gradual fashion, with the drip, drip, drip of point mutations accumulating along different lineages, and that leads to differentiation and new species,&rdquo said study coauthor William Martin of the Institute for Molecular Evolution at Heinrich-Heine-Universität in Germany. Traditional phylogenetic.

About a third of the archaeal genes analyzed had homologs among bacterial genomes, and the phylogenies of these apparent genetic imports closely mirrored those of archaeal-specific genes in each of 13 orders of archaea, suggesting that the birth of each order coincided with the gene acquisitions. “It seems like for each major branch of the archaea, the pivotal event that led to the isolation and specialization of each respective clade was the acquisition of a large number of bacterial genes,” said Eugene Koonin, who studies evolutionary genomics at the US National Center for Biotechnology Information. Koonin has collaborated with the study’s authors but was not involved in the present work.

Martin’s team first applied this analysis method to demonstrate that the salt-loving haloarchaeal group arose in concert with the acquisition of more than 1,000 bacterial genes, which conferred the ability to respire aerobically, among other metabolic functions. This analysis, published in PNAS in 2012, involved computing phylogenetic trees for 1,500 gene families. Constructing 25,000 trees for the present study was considerably more computationally intensive. “It’s a massive analysis—probably one of the larger tree-crunching exercises ever undertaken,” said W. Ford Doolittle of Dalhousie University in Canada, who was not involved in the study.

In particular, the phylogenies revealed that 83 percent of the bacterial introductions occurred in methanogenic archaea, which are thought by some to be the most ancient groups of archaea and have a simple metabolism—anaerobic reduction of carbon dioxide to methane in the presence of hydrogen gas. “People have suspected [the bacterial origin of many methanogen genes] for awhile,” said Doolittle. “Way back 15 years ago, when methanogen genomes started appearing, [these microbes] were the record holders for apparent import of bacterial genes.”

The conclusion that archaeal lineages abruptly picked up large groups of bacterial genes at the time of their formation, though supported by statistical tests, will require further analysis, Koonin noted. But the fact that 39 percent of the genetic imports analyzed by Martin’s team are involved in metabolism reinforces this idea. “It doesn’t make sense to incorporate one gene for the respiratory chain and not the others,” said Doolittle. “So biologically speaking, if they weren’t incorporated all at once, there would be no potential of incorporating some of them one at a time.”

R. Thane Papke of the University of Connecticut agreed that, while intriguing, the conclusions are not fully validated by the present analysis. “They’ve got some broad brushstrokes, it looks convincing, and I’m excited about it,” said Papke, who was not involved in the study. “More work just needs to be done.”

If the results hold up to further inquiry, however, the implications for scientists’ understanding of the early evolution of microbes could be huge. Martin compares the large-scale gene acquisitions in archaea to the origin of eukaryotes, which may have occurred when an archaeal cell incorporated a bacterial cell (along with its genes), which became the mitochondrion. “If this is widely accepted, it makes the origin of eukaryotes not as special,” said Doolittle. “That would be quite a paradigm shift in the way we think about things, because most people regard the origin of eukaryotes as a uniquely almost miraculous event.”

S. Nelson-Sathi et al., “Origins of major archaeal clades correspond to gene acquisitions from bacteria,” Nature, doi:10.1038/nature13805, 2014.