Articoli di riviste: "Lateral gene transfers"

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Andersson, Jan O., e Andrew J. Roger. "Evolutionary Analyses of the Small Subunit of Glutamate Synthase: Gene Order Conservation, Gene Fusions, and Prokaryote-to- Eukaryote Lateral Gene Transfers". Eukaryotic Cell 1, n. 2 (aprile 2002): 304–10. http://dx.doi.org/10.1128/ec.1.2.304-310.2002.

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ABSTRACT Lateral gene transfer has been identified as an important mode of genome evolution within prokaryotes. Except for the special case of gene transfer from organelle genomes to the eukaryotic nucleus, only a few cases of lateral gene transfer involving eukaryotes have been described. Here we present phylogenetic and gene order analyses on the small subunit of glutamate synthase (encoded by gltD) and its homologues, including the large subunit of sulfide dehydrogenase (encoded by sudA). The scattered distribution of the sudA and sudB gene pair and the phylogenetic analysis strongly suggest that lateral gene transfer was involved in the propagation of the genes in the three domains of life. One of these transfers most likely occurred between a prokaryote and an ancestor of diplomonad protists. Furthermore, phylogenetic analyses indicate that the gene for the small subunit of glutamate synthase was transferred from a low-GC gram-positive bacterium to a common ancestor of animals, fungi, and plants. Interestingly, in both examples, the eukaryotes encode a single gene that corresponds to a conserved operon structure in prokaryotes. Our analyses, together with several recent publications, show that lateral gene transfers from prokaryotes to unicellular eukaryotes occur with appreciable frequency. In the case of the genes for sulfide dehydrogenase, the transfer affected only a limited group of eukaryotes—the diplomonads—while the transfer of the glutamate synthase gene probably happened earlier in evolution and affected a wider range of eukaryotes.

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THUILLARD, MARC, e VINCENT MOULTON. "IDENTIFYING AND RECONSTRUCTING LATERAL TRANSFERS FROM DISTANCE MATRICES BY COMBINING THE MINIMUM CONTRADICTION METHOD AND NEIGHBOR-NET". Journal of Bioinformatics and Computational Biology 09, n. 04 (agosto 2011): 453–70. http://dx.doi.org/10.1142/s0219720011005409.

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Identifying lateral gene transfers is an important problem in evolutionary biology. Under a simple model of evolution, the expected values of an evolutionary distance matrix describing a phylogenetic tree fulfill the so-called Kalmanson inequalities. The Minimum Contradiction method for identifying lateral gene transfers exploits the fact that lateral transfers may generate large deviations from the Kalmanson inequalities. Here a new approach is presented to deal with such cases that combines the Neighbor-Net algorithm for computing phylogenetic networks with the Minimum Contradiction method. A subset of taxa, prescribed using Neighbor-Net, is obtained by measuring how closely the Kalmanson inequalities are fulfilled by each taxon. A criterion is then used to identify the taxa, possibly involved in a lateral transfer between nonconsecutive taxa. We illustrate the utility of the new approach by applying it to a distance matrix for Archaea, Bacteria, and Eukaryota.

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Tofigh, A., M. Hallett e J. Lagergren. "Simultaneous Identification of Duplications and Lateral Gene Transfers". IEEE/ACM Transactions on Computational Biology and Bioinformatics 8, n. 2 (marzo 2011): 517–35. http://dx.doi.org/10.1109/tcbb.2010.14.

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Marri, Pradeep Reddy, John P. Bannantine, Michael L. Paustian e G. Brian Golding. "Lateral gene transfer in Mycobacterium avium subspecies paratuberculosis". Canadian Journal of Microbiology 52, n. 6 (1 giugno 2006): 560–69. http://dx.doi.org/10.1139/w06-001.

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Lateral gene transfer is an integral part of genome evolution in most bacteria. Bacteria can readily change the contents of their genomes to increase adaptability to ever-changing surroundings and to generate evolutionary novelty. Here, we report instances of lateral gene transfer in Mycobacterium avium subsp. paratuberculosis, a pathogenic bacteria that causes Johne's disease in cattle. A set of 275 genes are identified that are likely to have been recently acquired by lateral gene transfer. The analysis indicated that 53 of the 275 genes were acquired after the divergence of M. avium subsp. paratuberculosis from M. avium subsp. avium, whereas the remaining 222 genes were possibly acquired by a common ancestor of M. avium subsp. paratuberculosis and M. avium subsp. avium after its divergence from the ancestor of M. tuberculosis complex. Many of the acquired genes were from proteobacteria or soil dwelling actinobacteria. Prominent among the predicted laterally transferred genes is the gene rsbR, a possible regulator of sigma factor, and the genes designated MAP3614 and MAP3757, which are similar to genes in eukaryotes. The results of this study suggest that like most other bacteria, lateral gene transfers seem to be a common feature in M. avium subsp. paratuberculosis and that the proteobacteria contribute most of these genetic exchanges.Key words: mycobacteria, M. avium subsp. paratuberculosis, lateral gene transfer, unique genes, phylogeny.

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Zhi-Zhong Chen, Fei Deng e Lusheng Wang. "Simultaneous Identification of Duplications, Losses, and Lateral Gene Transfers". IEEE/ACM Transactions on Computational Biology and Bioinformatics 9, n. 5 (settembre 2012): 1515–28. http://dx.doi.org/10.1109/tcbb.2012.79.

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Yubuki, Naoji, Luis Javier Galindo, Guillaume Reboul, Purificación López-García, Matthew W. Brown, Nicolas Pollet e David Moreira. "Ancient Adaptive Lateral Gene Transfers in the Symbiotic Opalina–Blastocystis Stramenopile Lineage". Molecular Biology and Evolution 37, n. 3 (6 novembre 2019): 651–59. http://dx.doi.org/10.1093/molbev/msz250.

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Abstract Lateral gene transfer is a very common process in bacterial and archaeal evolution, playing an important role in the adaptation to new environments. In eukaryotes, its role and frequency remain highly debated, although recent research supports that gene transfer from bacteria to diverse eukaryotes may be much more common than previously appreciated. However, most of this research focused on animals and the true phylogenetic and functional impact of bacterial genes in less-studied microbial eukaryotic groups remains largely unknown. Here, we have analyzed transcriptome data from the deep-branching stramenopile Opalinidae, common members of frog gut microbiomes, and distantly related to the well-known genus Blastocystis. Phylogenetic analyses suggest the early acquisition of several bacterial genes in a common ancestor of both lineages. Those lateral gene transfers most likely facilitated the adaptation of the free-living ancestor of the Opalinidae–Blastocystis symbiotic group to new niches in the oxygen-depleted animal gut environment.

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Friedrich, Michael W. "Phylogenetic Analysis Reveals Multiple Lateral Transfers of Adenosine-5′-Phosphosulfate Reductase Genes among Sulfate-Reducing Microorganisms". Journal of Bacteriology 184, n. 1 (1 gennaio 2002): 278–89. http://dx.doi.org/10.1128/jb.184.1.278-289.2002.

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ABSTRACT Lateral gene transfer affects the evolutionary path of key genes involved in ancient metabolic traits, such as sulfate respiration, even more than previously expected. In this study, the phylogeny of the adenosine-5′-phosphosulfate (APS) reductase was analyzed. APS reductase is a key enzyme in sulfate respiration present in all sulfate-respiring prokaryotes. A newly developed PCR assay was used to amplify and sequence a fragment (∼900 bp) of the APS reductase gene, apsA, from a taxonomically wide range of sulfate-reducing prokaryotes (n = 60). Comparative phylogenetic analysis of all obtained and available ApsA sequences indicated a high degree of sequence conservation in the region analyzed. However, a comparison of ApsA- and 16S rRNA-based phylogenetic trees revealed topological incongruences affecting seven members of the Syntrophobacteraceae and three members of the Nitrospinaceae, which were clearly monophyletic with gram-positive sulfate-reducing bacteria (SRB). In addition, Thermodesulfovibrio islandicus and Thermodesulfobacterium thermophilum, Thermodesulfobacterium commune, and Thermodesulfobacterium hveragerdense clearly branched off between the radiation of the δ-proteobacterial gram-negative SRB and the gram-positive SRB and not close to the root of the tree as expected from 16S rRNA phylogeny. The most parsimonious explanation for these discrepancies in tree topologies is lateral transfer of apsA genes across bacterial divisions. Similar patterns of insertions and deletions in ApsA sequences of donor and recipient lineages provide additional evidence for lateral gene transfer. From a subset of reference strains (n = 25), a fragment of the dissimilatory sulfite reductase genes (dsrAB), which have recently been proposed to have undergone multiple lateral gene transfers (M. Klein et al., J. Bacteriol. 183:6028–6035, 2001), was also amplified and sequenced. Phylogenetic comparison of DsrAB- and ApsA-based trees suggests a frequent involvement of gram-positive and thermophilic SRB in lateral gene transfer events among SRB.

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Abby, Sophie S., Eric Tannier, Manolo Gouy e Vincent Daubin. "Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests". BMC Bioinformatics 11, n. 1 (2010): 324. http://dx.doi.org/10.1186/1471-2105-11-324.

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Alsmark, Cecilia, Peter G. Foster, Thomas Sicheritz-Ponten, Sirintra Nakjang, T. Martin Embley e Robert P. Hirt. "Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes". Genome Biology 14, n. 2 (2013): R19. http://dx.doi.org/10.1186/gb-2013-14-2-r19.

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Gophna, Uri. "Complexity Apparently Is Not a Barrier to Lateral Gene Transfers". Microbe Magazine 4, n. 12 (1 dicembre 2009): 549–53. http://dx.doi.org/10.1128/microbe.4.549.1.

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Nesbø, Camilla L., Eric Bapteste, Bruce Curtis, Håkon Dahle, Philippe Lopez, Dave Macleod, Marlena Dlutek et al. "The Genome of Thermosipho africanus TCF52B: Lateral Genetic Connections to the Firmicutes and Archaea". Journal of Bacteriology 191, n. 6 (5 gennaio 2009): 1974–78. http://dx.doi.org/10.1128/jb.01448-08.

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ABSTRACT Lateral gene transfers (LGT) (also called horizontal gene transfers) have been a major force shaping the Thermosipho africanus TCF52B genome, whose sequence we describe here. Firmicutes emerge as the principal LGT partner. Twenty-six percent of phylogenetic trees suggest LGT with this group, while 13% of the open reading frames indicate LGT with Archaea.

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Naumoff, D. G., e S. N. Dedysh. "Glycoside Hydrolases of the Obligate Methanotroph <i>Methyloferula stellata</i>: an Unusual Evolutionary Strategy not Involving Distant Lateral Transfers". Микробиология 92, n. 3 (1 maggio 2023): 243–49. http://dx.doi.org/10.31857/s002636562260078x.

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Abstract—The genome of the obligately methanotrophic bacterium Methyloferula stellata AR4 encodes thirty glycoside hydrolases. The closest homologues for most of these proteins belong to other members of the class Alphaproteobacteria. Two exceptions are represented by the genes encoding glycoside hydrolases of the families GH39 and GH65, which presumably appeared in M. stellata AR4 due to the lateral transfer from distantly related bacteria. This work was devoted to the study of the evolutionary history of these two genes. In the case of a member of the GH65 family of glycoside hydrolases, this scenario was not confirmed. Kojibiose phosphorylase encoded by this gene is common among Alphaproteobacteria. The suggested lateral transfer of the corresponding gene had an opposite direction, into one of the evolutionary lineages of the class Betaproteobacteria. The potential glycoside hydrolase of the GH39 family was shown to be the only one which gene is not of proteobacterial origin. The role of lateral transfers in the evolution of glycoside hydrolases and their homologues in methanotrophs and other bacteria is discussed.

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Katz, L. A. "Lateral gene transfers and the evolution of eukaryotes: theories and data". INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 52, n. 5 (1 settembre 2002): 1893–900. http://dx.doi.org/10.1099/ijs.0.02113-0.

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Katz, Laura A. "Lateral gene transfers and the evolution of eukaryotes: theories and data." International Journal of Systematic and Evolutionary Microbiology 52, n. 5 (1 settembre 2002): 1893–900. http://dx.doi.org/10.1099/00207713-52-5-1893.

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Katz, Laura A. "Recent events dominate interdomain lateral gene transfers between prokaryotes and eukaryotes and, with the exception of endosymbiotic gene transfers, few ancient transfer events persist". Philosophical Transactions of the Royal Society B: Biological Sciences 370, n. 1678 (26 settembre 2015): 20140324. http://dx.doi.org/10.1098/rstb.2014.0324.

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While there is compelling evidence for the impact of endosymbiotic gene transfer (EGT; transfer from either mitochondrion or chloroplast to the nucleus) on genome evolution in eukaryotes, the role of interdomain transfer from bacteria and/or archaea (i.e. prokaryotes) is less clear. Lateral gene transfers (LGTs) have been argued to be potential sources of phylogenetic information, particularly for reconstructing deep nodes that are difficult to recover with traditional phylogenetic methods. We sought to identify interdomain LGTs by using a phylogenomic pipeline that generated 13 465 single gene trees and included up to 487 eukaryotes, 303 bacteria and 118 archaea. Our goals include searching for LGTs that unite major eukaryotic clades, and describing the relative contributions of LGT and EGT across the eukaryotic tree of life. Given the difficulties in interpreting single gene trees that aim to capture the approximately 1.8 billion years of eukaryotic evolution, we focus on presence–absence data to identify interdomain transfer events. Specifically, we identify 1138 genes found only in prokaryotes and representatives of three or fewer major clades of eukaryotes (e.g. Amoebozoa, Archaeplastida, Excavata, Opisthokonta, SAR and orphan lineages). The majority of these genes have phylogenetic patterns that are consistent with recent interdomain LGTs and, with the notable exception of EGTs involving photosynthetic eukaryotes, we detect few ancient interdomain LGTs. These analyses suggest that LGTs have probably occurred throughout the history of eukaryotes, but that ancient events are not maintained unless they are associated with endosymbiotic gene transfer among photosynthetic lineages.

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Liapounova, Natalia A., Vladimir Hampl, Paul M. K. Gordon, Christoph W. Sensen, Lashitew Gedamu e Joel B. Dacks. "Reconstructing the Mosaic Glycolytic Pathway of the Anaerobic Eukaryote Monocercomonoides". Eukaryotic Cell 5, n. 12 (27 ottobre 2006): 2138–46. http://dx.doi.org/10.1128/ec.00258-06.

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ABSTRACT All eukaryotes carry out glycolysis, interestingly, not all using the same enzymes. Anaerobic eukaryotes face the challenge of fewer molecules of ATP extracted per molecule of glucose due to their lack of a complete tricarboxylic acid cycle. This may have pressured anaerobic eukaryotes to acquire the more ATP-efficient alternative glycolytic enzymes, such as pyrophosphate-fructose 6-phosphate phosphotransferase and pyruvate orthophosphate dikinase, through lateral gene transfers from bacteria and other eukaryotes. Most studies of these enzymes in eukaryotes involve pathogenic anaerobes; Monocercomonoides, an oxymonad belonging to the eukaryotic supergroup Excavata, is a nonpathogenic anaerobe representing an evolutionarily and ecologically distinct sampling of an anaerobic glycolytic pathway. We sequenced cDNA encoding glycolytic enzymes from a previously established cDNA library of Monocercomonoides and analyzed the relationships of these enzymes to those from other organisms spanning the major groups of Eukaryota, Bacteria, and Archaea. We established that, firstly, Monocercomonoides possesses alternative versions of glycolytic enzymes: fructose-6-phosphate phosphotransferase, both pyruvate kinase and pyruvate orthophosphate dikinase, cofactor-independent phosphoglycerate mutase, and fructose-bisphosphate aldolase (class II, type B). Secondly, we found evidence for the monophyly of oxymonads, kinetoplastids, diplomonads, and parabasalids, the major representatives of the Excavata. We also found several prokaryote-to-eukaryote as well as eukaryote-to-eukaryote lateral gene transfers involving glycolytic enzymes from anaerobic eukaryotes, further suggesting that lateral gene transfer was an important factor in the evolution of this pathway for denizens of this environment.

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Szöllősi, Gergely J., Adrián Arellano Davín, Eric Tannier, Vincent Daubin e Bastien Boussau. "Genome-scale phylogenetic analysis finds extensive gene transfer among fungi". Philosophical Transactions of the Royal Society B: Biological Sciences 370, n. 1678 (26 settembre 2015): 20140335. http://dx.doi.org/10.1098/rstb.2014.0335.

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Although the role of lateral gene transfer is well recognized in the evolution of bacteria, it is generally assumed that it has had less influence among eukaryotes. To explore this hypothesis, we compare the dynamics of genome evolution in two groups of organisms: cyanobacteria and fungi. Ancestral genomes are inferred in both clades using two types of methods: first, Count , a gene tree unaware method that models gene duplications, gains and losses to explain the observed numbers of genes present in a genome; second, ALE, a more recent gene tree-aware method that reconciles gene trees with a species tree using a model of gene duplication, loss and transfer. We compare their merits and their ability to quantify the role of transfers, and assess the impact of taxonomic sampling on their inferences. We present what we believe is compelling evidence that gene transfer plays a significant role in the evolution of fungi.

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Oliver, Richard P., e Peter S. Solomon. "Recent Fungal Diseases of Crop Plants: Is Lateral Gene Transfer a Common Theme?" Molecular Plant-Microbe Interactions® 21, n. 3 (marzo 2008): 287–93. http://dx.doi.org/10.1094/mpmi-21-3-0287.

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A cursory glance at old textbooks of plant pathology reveals that the diseases which are the current scourge of agriculture in many parts of the world are a different set from those that were prominent 50 or 100 years ago. Why have these new diseases arisen? The traditional explanations subscribe to the “nature abhors a vacuum” principle—that control of one disease creates the condition for the emergence of a replacement—but does little to explain why the new pathogen succeeds. The emergence of a new disease requires a series of conditions and steps, including the enhanced fecundity of the new pathogen, enhanced survival from season to season, and spread around the world. Recently, evidence was obtained that wheat tan spot emerged through a lateral gene transfer event some time prior to 1941. Although there have been sporadic and persistent reports of lateral gene transfer between and into fungal plant pathogens, most examples have been dismissed through incomplete evidence. The completion of whole genome sequences of an increasing number of fungal pathogens no longer allows such proposed cases of lateral gene transfer to be dismissed so easily. How frequent are lateral gene transfers involving fungal plant pathogens, and can this process explain the emergence of many of the new diseases of the recent past? Many of the apparently new diseases are dependant on the expression of host-specific toxins. These are enigmatic molecules whose action requires the presence of plant genes with products that specifically encode sensitivity to the toxin and susceptibility to the disease. It is also notable that many new diseases belong to the fungal taxon dothideomycetes. This review explores the coincidence of new diseases, interspecific gene transfer, host-specific toxins, and the dothideomycete class.

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Andersson, Jan O., Åsa M. Sjögren, Lesley A. M. Davis, T. Martin Embley e Andrew J. Roger. "Phylogenetic Analyses of Diplomonad Genes Reveal Frequent Lateral Gene Transfers Affecting Eukaryotes". Current Biology 13, n. 2 (gennaio 2003): 94–104. http://dx.doi.org/10.1016/s0960-9822(03)00003-4.

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Parker, Matthew A., e David A. Kennedy. "Diversity and relationships of bradyrhizobia from legumes native to eastern North America". Canadian Journal of Microbiology 52, n. 12 (1 dicembre 2006): 1148–57. http://dx.doi.org/10.1139/w06-076.

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DNA sequencing and polymerase chain reaction (PCR) assays with lineage-specific primers were used to analyze the diversity of 276 isolates of Bradyrhizobium sp. nodule bacteria associated with 13 native legumes species in the northeastern United States, representing eight genera in six legume tribes. A PCR screen with two primer pairs in the rRNA region indicated that seven of the legume species were exclusively associated with strains having markers resembling Bradyrhizobium elkanii, while the remaining six host species harbored strains related to both B. elkanii and Bradyrhizobium japonicum. Sequence analysis of 22 isolates for portions of 16S rRNA and 23S rRNA yielded congruent phylogenetic trees and showed that isolates from different legume genera often shared similar or identical sequences. However, trees inferred from portions of two other genes (α-ketoglutarate dioxygenase gene (tfdA), the α-subunit of nitrogenase (nifD)) differed significantly from the rRNA phylogeny. Thus, for Bradyrhizobium populations in this region, lateral gene transfer events appear to have altered genealogical relationships of different portions of the genome. These results extend the number of likely cases of gene transfer between divergent taxa of Bradyrhizobium (from members of the B. elkanii lineage to the B. japonicum group) and suggest that transfers have also occurred among separate subgroups of the B. elkanii lineage.Key words: Bradyrhizobiaceae, lateral gene transfer, phylogenetic congruence, ribosomal RNA.

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Danchin, Etienne G. J., Marie-Noëlle Rosso, Paulo Vieira, Janice de Almeida-Engler, Pedro M. Coutinho, Bernard Henrissat e Pierre Abad. "Multiple lateral gene transfers and duplications have promoted plant parasitism ability in nematodes". Proceedings of the National Academy of Sciences 107, n. 41 (27 settembre 2010): 17651–56. http://dx.doi.org/10.1073/pnas.1008486107.

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Romero, Miguel, R. Cerritos e Cecilia Ximenez. "Horizontal Gene Transfers from Bacteria toEntamoebaComplex: A Strategy for Dating Events along Species Divergence". Journal of Parasitology Research 2016 (2016): 1–10. http://dx.doi.org/10.1155/2016/3241027.

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Horizontal gene transfer has proved to be relevant in eukaryotic evolution, as it has been found more often than expected and related to adaptation to certain niches. A relatively large list of laterally transferred genes has been proposed and evaluated for the parasiteEntamoeba histolytica. The goals of this work were to elucidate the importance of lateral gene transfer along the evolutionary history of some members of the genusEntamoeba, through identifying donor groups and estimating the divergence time of some of these events. In order to estimate the divergence time of some of the horizontal gene transfer events, the dating of someEntamoebaspecies was necessary, following an indirect dating strategy based on the fossil record of plausible hosts. The divergence betweenE. histolyticaandE. nuttalliiprobably occurred 5.93 million years ago (Mya); this lineage diverged fromE. dispar9.97 Mya, while the ancestor of the latter separated fromE. invadens68.18 Mya. We estimated times for 22 transferences; the most recent occurred 31.45 Mya and the oldest 253.59 Mya. Indeed, the acquisition of genes through lateral transfer may have triggered a period of adaptive radiation, thus playing a major role in the evolution of theEntamoebagenus.

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Olofsson, Jill K., Luke T. Dunning, Marjorie R. Lundgren, Henry J. Barton, John Thompson, Nicholas Cuff, Menaka Ariyarathne et al. "Population-Specific Selection on Standing Variation Generated by Lateral Gene Transfers in a Grass". Current Biology 29, n. 22 (novembre 2019): 3921–27. http://dx.doi.org/10.1016/j.cub.2019.09.023.

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Dunning, Luke T., Jill K. Olofsson, Christian Parisod, Rimjhim Roy Choudhury, Jose J. Moreno-Villena, Yang Yang, Jacqueline Dionora et al. "Lateral transfers of large DNA fragments spread functional genes among grasses". Proceedings of the National Academy of Sciences 116, n. 10 (20 febbraio 2019): 4416–25. http://dx.doi.org/10.1073/pnas.1810031116.

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A fundamental tenet of multicellular eukaryotic evolution is that vertical inheritance is paramount, with natural selection acting on genetic variants transferred from parents to offspring. This lineal process means that an organism’s adaptive potential can be restricted by its evolutionary history, the amount of standing genetic variation, and its mutation rate. Lateral gene transfer (LGT) theoretically provides a mechanism to bypass many of these limitations, but the evolutionary importance and frequency of this process in multicellular eukaryotes, such as plants, remains debated. We address this issue by assembling a chromosome-level genome for the grassAlloteropsis semialata, a species surmised to exhibit two LGTs, and screen it for other grass-to-grass LGTs using genomic data from 146 other grass species. Through stringent phylogenomic analyses, we discovered 57 additional LGTs in theA. semialatanuclear genome, involving at least nine different donor species. The LGTs are clustered in 23 laterally acquired genomic fragments that are up to 170 kb long and have accumulated during the diversification ofAlloteropsis.The majority of the 59 LGTs inA. semialataare expressed, and we show that they have added functions to the recipient genome. Functional LGTs were further detected in the genomes of five other grass species, demonstrating that this process is likely widespread in this globally important group of plants. LGT therefore appears to represent a potent evolutionary force capable of spreading functional genes among distantly related grass species.

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Hirt, Robert P., Cecilia Alsmark e T. Martin Embley. "Lateral gene transfers and the origins of the eukaryote proteome: a view from microbial parasites". Current Opinion in Microbiology 23 (febbraio 2015): 155–62. http://dx.doi.org/10.1016/j.mib.2014.11.018.

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Klein, Michael, Michael Friedrich, Andrew J. Roger, Philip Hugenholtz, Susan Fishbain, Heike Abicht, Linda L. Blackall, David A. Stahl e Michael Wagner. "Multiple Lateral Transfers of Dissimilatory Sulfite Reductase Genes between Major Lineages of Sulfate-Reducing Prokaryotes". Journal of Bacteriology 183, n. 20 (15 ottobre 2001): 6028–35. http://dx.doi.org/10.1128/jb.183.20.6028-6035.2001.

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ABSTRACT A large fragment of the dissimilatory sulfite reductase genes (dsrAB) was PCR amplified and fully sequenced from 30 reference strains representing all recognized lineages of sulfate-reducing bacteria. In addition, the sequence of thedsrAB gene homologs of the sulfite reducerDesulfitobacterium dehalogenans was determined. In contrast to previous reports, comparative analysis of all available DsrAB sequences produced a tree topology partially inconsistent with the corresponding 16S rRNA phylogeny. For example, the DsrAB sequences of several Desulfotomaculum species (low G+C gram-positive division) and two members of the genusThermodesulfobacterium (a separate bacterial division) were monophyletic with δ-proteobacterial DsrAB sequences. The most parsimonious interpretation of these data is thatdsrAB genes from ancestors of as-yet-unrecognized sulfate reducers within the δ-Proteobacteria were laterally transferred across divisions. A number of insertions and deletions in the DsrAB alignment independently support these inferred lateral acquisitions of dsrAB genes. Evidence for adsrAB lateral gene transfer event also was found within the δ-Proteobacteria, affecting Desulfobacula toluolica. The root of the dsr tree was inferred to be within the Thermodesulfovibrio lineage by paralogous rooting of the alpha and beta subunits. This rooting suggests that the dsrAB genes inArchaeoglobus species also are the result of an ancient lateral transfer from a bacterial donor. Although these findings complicate the use of dsrAB genes to infer phylogenetic relationships among sulfate reducers in molecular diversity studies, they establish a framework to resolve the origins and diversification of this ancient respiratory lifestyle among organisms mediating a key step in the biogeochemical cycling of sulfur.

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Bodilis, Josselin, Sandrine Nsigue-Meilo, Ludovic Besaury e Laurent Quillet. "Variable Copy Number, Intra-Genomic Heterogeneities and Lateral Transfers of the 16S rRNA Gene in Pseudomonas". PLoS ONE 7, n. 4 (24 aprile 2012): e35647. http://dx.doi.org/10.1371/journal.pone.0035647.

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Foster, Jeremy M., Paul J. Davis, Sylvine Raverdy, Marion H. Sibley, Elisabeth A. Raleigh, Sanjay Kumar e Clotilde K. S. Carlow. "Evolution of Bacterial Phosphoglycerate Mutases: Non-Homologous Isofunctional Enzymes Undergoing Gene Losses, Gains and Lateral Transfers". PLoS ONE 5, n. 10 (26 ottobre 2010): e13576. http://dx.doi.org/10.1371/journal.pone.0013576.

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Paganini, Julien, Amandine Campan-Fournier, Martine Da Rocha, Philippe Gouret, Pierre Pontarotti, Eric Wajnberg, Pierre Abad e Etienne G. J. Danchin. "Contribution of Lateral Gene Transfers to the Genome Composition and Parasitic Ability of Root-Knot Nematodes". PLoS ONE 7, n. 11 (30 novembre 2012): e50875. http://dx.doi.org/10.1371/journal.pone.0050875.

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Watkins, Russell F., e Michael W. Gray. "The Frequency of Eubacterium-to-Eukaryote Lateral Gene Transfers Shows Significant Cross-Taxa Variation Within Amoebozoa". Journal of Molecular Evolution 63, n. 6 (2 novembre 2006): 801–14. http://dx.doi.org/10.1007/s00239-006-0031-0.

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Niklas, Karl J., e Ulrich Kutschera. "The evolutionary development of plant body plans". Functional Plant Biology 36, n. 8 (2009): 682. http://dx.doi.org/10.1071/fp09107.

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Evolutionary developmental biology, cladistic analyses, and paleontological insights make it increasingly clear that regulatory mechanisms operating during embryogenesis and early maturation tend to be highly conserved over great evolutionary time scales, which can account for the conservative nature of the body plans in the major plant and animal clades. At issue is whether morphological convergences in body plans among evolutionarily divergent lineages are the result of adaptive convergence or ‘genome recall’ and ‘process orthology’. The body plans of multicellular photosynthetic eukaryotes (‘plants’) are reviewed, some of their important developmental/physiological regulatory mechanisms discussed, and the evidence that some of these mechanisms are phyletically ancient examined. We conclude that endosymbiotic lateral gene transfers, gene duplication and functional divergence, and the co-option of ancient gene networks were key to the evolutionary divergence of plant lineages.

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Coombs, J. M., e T. Barkay. "Molecular Evidence for the Evolution of Metal Homeostasis Genes by Lateral Gene Transfer in Bacteria from the Deep Terrestrial Subsurface". Applied and Environmental Microbiology 70, n. 3 (marzo 2004): 1698–707. http://dx.doi.org/10.1128/aem.70.3.1698-1707.2004.

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ABSTRACT Lateral gene transfer (LGT) plays a vital role in increasing the genetic diversity of microorganisms and promoting the spread of fitness-enhancing phenotypes throughout microbial communities. To date, LGT has been investigated in surface soils, natural waters, and biofilm communities but not in the deep terrestrial subsurface. Here we used a combination of molecular analyses to investigate the role of LGT in the evolution of metal homeostasis in lead-resistant subsurface bacteria. A nested PCR approach was employed to obtain DNA sequences encoding PIB-type ATPases, which are proteins that transport toxic or essential soft metals such as Zn(II), Cd(II), and Pb(II) through the cell wall. Phylogenetic incongruencies between a 16S rRNA gene tree and a tree based on 48 PIB-type ATPase amplicons and sequences available for complete bacterial genomes revealed an ancient transfer from a member of the β subclass of the Proteobacteria (β-proteobacterium) that may have predated the diversification of the genus Pseudomonas. Four additional phylogenetic incongruencies indicate that LGT has occurred among groups of β- and γ-proteobacteria. Two of these transfers appeared to be recent, as indicated by an unusual G+C content of the PIB-type ATPase amplicons. This finding provides evidence that LGT plays a distinct role in the evolution of metal homeostasis in deep subsurface bacteria, and it shows that molecular evolutionary approaches may be used for investigation of this process in microbial communities in specific environments.

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Brochier-Armanet, Céline, e Patrick Forterre. "Widespread distribution of archaeal reverse gyrase in thermophilic bacteria suggests a complex history of vertical inheritance and lateral gene transfers". Archaea 2, n. 2 (2006): 83–93. http://dx.doi.org/10.1155/2006/582916.

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Reverse gyrase, an enzyme of uncertain funtion, is present in all hyperthermophilic archaea and bacteria. Previous phylogenetic studies have suggested that the gene for reverse gyrase has an archaeal origin and was transferred laterally (LGT) to the ancestors of the two bacterial hyperthermophilic phyla, Thermotogales and Aquificales. Here, we performed an in-depth analysis of the evolutionary history of reverse gyrase in light of genomic progress. We found genes coding for reverse gyrase in the genomes of several thermophilic bacteria that belong to phyla other than Aquificales and Thermotogales. Several of these bacteria are not, strictly speaking, hyperthermophiles because their reported optimal growth temperatures are below 80 °C. Furthermore, we detected a reverse gyrase gene in the sequence of the large plasmid ofThermus thermophilusstrain HB8, suggesting a possible mechanism of transfer to theT. thermophilusstrain HB8 involving plasmids and transposases. The archaeal part of the reverse gyrase tree is congruent with recent phylogenies of the archaeal domain based on ribosomal proteins or RNA polymerase subunits. Although poorly resolved, the complete reverse gyrase phylogeny suggests an ancient acquisition of the gene by bacteria via one or two LGT events, followed by its secondary distribution by LGT within bacteria. Finally, several genes of archaeal origin located in proximity to the reverse gyrase gene in bacterial genomes have bacterial homologues mostly in thermophiles or hyperthermophiles, raising the possibility that they were co-transferred with the reverse gyrase gene. Our new analysis of the reverse gyrase history strengthens the hypothesis that the acquisition of reverse gyrase may have been a crucial evolutionary step in the adaptation of bacteria to high-temperature environments. However, it also questions the role of this enzyme in thermophilic bacteria and the selective advantage its presence could provide.

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Sen, Arnab, Vincent Daubin, Danis Abrouk, Isaac Gifford, Alison M. Berry e Philippe Normand. "Phylogeny of the class Actinobacteria revisited in the light of complete genomes. The orders ‘Frankiales’ and Micrococcales should be split into coherent entities: proposal of Frankiales ord. nov., Geodermatophilales ord. nov., Acidothermales ord. nov. and Nakamurellales ord. nov." International Journal of Systematic and Evolutionary Microbiology 64, Pt_11 (1 novembre 2014): 3821–32. http://dx.doi.org/10.1099/ijs.0.063966-0.

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The phylogeny of the class Actinobacteria remains controversial, essentially because it is very sensitive to the choice of dataset and phylogenetic methods. We used a test proposed recently, based on complete genome data, which chooses among candidate species phylogenies based on the number of lateral gene transfers (LGT) needed to explain the diversity of histories among gene trees for a set of genomes. We used 100 completely sequenced genomes representing 35 families and 17 orders of the class Actinobacteria and evaluated eight different hypotheses for their phylogeny, including one based on a concatenate of 54 conserved proteins present in single copy in all these genomes, trees based on 16S and 23S rRNA gene sequences or their concatenation, and a tree based on the concatenation of MLSA genes (encoding AtpI, GyrA, FtsZ, SecA and DnaK). We used Prunier to infer the number of LGT in 579 proteins (different from those used to build the concatenated tree) present in at least 70 species, using the different hypothetical species trees as references. The best tree, with the lowest number of lateral transfers, was the one based on the concatenation of 54 proteins. In that tree, the orders Bifidobacteriales , Coriobacteriales , ‘Coryneb acteriales’, ‘Micromonosporales’, ‘Propionibacteriales’, ‘Pseudonocardiales’, Streptomycetales and ‘Streptosporangiales’ were recovered while the orders ‘Frankiales’ and Micrococcales were not. It is thus proposed that the order ‘Frankiales’, which has an effectively but not validly published name, be split into Frankiales ord. nov. (type family Frankiaceae ), Geodermatophilales ord. nov. ( Geodermatophilaceae ), Acidothermales ord. nov. ( Acidothermaceae ) and Nakamurellales ord. nov. ( Nakamurellaceae ). The order Micrococcales should also be split into Micrococcales (genera Kocuria , Rothia , Micrococcus , Arthrobacter , Tropheryma , Microbacterium , Leifsonia and Clavibacter ), Cellulomonales ( Beutenbergia , Cellulomonas , Xylanimonas , Jonesia and Sanguibacter ) and Brachybacteriales ( Brachybacterium ) but the formal proposal for this will have to wait until more genomes become available for a significant proportion of strains in this order.

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Kalyuzhnaya, Marina G., Natalia Korotkova, Gregory Crowther, Christopher J. Marx, Mary E. Lidstrom e Ludmila Chistoserdova. "Analysis of Gene Islands Involved in Methanopterin-Linked C1 Transfer Reactions Reveals New Functions and Provides Evolutionary Insights". Journal of Bacteriology 187, n. 13 (1 luglio 2005): 4607–14. http://dx.doi.org/10.1128/jb.187.13.4607-4614.2005.

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ABSTRACT In this study, the occurrence and chromosomal clustering of genes encoding C1 transfer reactions linked to tetrahydromethanopterin (H4MPT) were analyzed in a variety of proteobacteria and in representatives of the Planctomycetes via genomic analysis or via partial sequencing by cosmid walking. Although a tendency for clustering was found common for the genes of interest, significant variations in gene order and the degree of clustering were uncovered both between and within different groups of Proteobacteria and between Proteobacteria and Planctomycetes. Phylogenetic analyses suggested that the evolution of genes encoding H4MPT-linked reactions in Proteobacteria involved lateral transfers within Proteobacteria and possibly between Proteobacteria and other phyla. Gene cluster comparisons revealed a number of novel genes potentially involved in the C1 transfer reactions, and these were analyzed by mutation and expression analyses. Four genes, a homolog of pabB, and three genes conserved between methanogenic Archaea and Bacteria possessing H4MPT-linked functions, orfY, orf1, and afpA were shown to be involved in formaldehyde oxidation/detoxification, as judged by specific mutant phenotypes. In particular, pabB contributes to the biosynthesis of para-aminobenzoic acid, a precursor of both tetrahydrofolate and H4MPT, and afpA apparently encodes a novel dihydromethanopterin reductase, based on mutant complementation experiments.

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Mukai, Atsushi, e Hiroshi Endoh. "Presence of a Bacterial-Like Citrate Synthase Gene in Tetrahymena thermophila : Recent Lateral Gene Transfers (LGT) or Multiple Gene Losses Subsequent to a Single Ancient LGT?" Journal of Molecular Evolution 58, n. 5 (1 maggio 2004): 540–49. http://dx.doi.org/10.1007/s00239-003-2576-5.

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Hafez, Mohamed, e Georg Hausner. "Homing endonucleases: DNA scissors on a mission". Genome 55, n. 8 (agosto 2012): 553–69. http://dx.doi.org/10.1139/g2012-049.

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Buried within the genomes of many microorganisms are genetic elements that encode rare-cutting homing endonucleases that assist in the mobility of the elements that encode them, such as the self-splicing group I and II introns and in some cases inteins. There are several different families of homing endonucleases and their ability to initiate and target specific sequences for lateral transfers makes them attractive reagents for gene targeting. Homing endonucleases have been applied in promoting DNA modification or genome editing such as gene repair or “gene knockouts”. This review examines the categories of homing endonucleases that have been described so far and their possible applications to biotechnology. Strategies to engineer homing endonucleases to alter target site specificities will also be addressed. Alternatives to homing endonucleases such as zinc finger nucleases, transcription activator-like effector nucleases, triplex forming oligonucleotide nucleases, and targetrons are also briefly discussed.

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Guidot, Alice, Philippe Prior, Jens Schoenfeld, Sébastien Carrère, Stéphane Genin e Christian Boucher. "Genomic Structure and Phylogeny of the Plant Pathogen Ralstonia solanacearum Inferred from Gene Distribution Analysis". Journal of Bacteriology 189, n. 2 (3 novembre 2006): 377–87. http://dx.doi.org/10.1128/jb.00999-06.

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ABSTRACT In the present study, we investigated the gene distribution among strains of the highly polymorphic plant pathogenic β-proteobacterium Ralstonia solanacearum, paying particular attention to the status of known or candidate pathogenicity genes. Based on the use of comparative genomic hybridization on a pangenomic microarray for the GMI1000 reference strain, we have defined the conditions that allowed comparison of the repertoires of genes among a collection of 18 strains that are representative of the biodiversity of the R. solanacearum species. This identified a list of 2,690 core genes present in all tested strains. As a corollary, a list of 2,338 variable genes within the R. solanacearum species has been defined. The hierarchical clustering based on the distribution of variable genes is fully consistent with the phylotype classification that was previously defined from the nucleotide sequence analysis of four genes. The presence of numerous pathogenicity-related genes in the core genome indicates that R. solanacearum is an ancestral pathogen. The results establish the long coevolution of the two replicons that constitute the bacterial genome. We also demonstrate the clustering of variable genes in genomic islands. Most genomic islands are included in regions with an alternative codon usage, suggesting that they originate from acquisition of foreign genes through lateral gene transfers. Other genomic islands correspond to genes that have the same base composition as core genes, suggesting that they either might be ancestral genes lost by deletion in certain strains or might originate from horizontal gene transfers.

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Moreau, Hervé, Gwenael Piganeau, Yves Desdevises, Richard Cooke, Evelyne Derelle e Nigel Grimsley. "Marine Prasinovirus Genomes Show Low Evolutionary Divergence and Acquisition of Protein Metabolism Genes by Horizontal Gene Transfer". Journal of Virology 84, n. 24 (22 settembre 2010): 12555–63. http://dx.doi.org/10.1128/jvi.01123-10.

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ABSTRACT Although marine picophytoplankton are at the base of the global food chain, accounting for half of the planetary primary production, they are outnumbered 10 to 1 and are largely controlled by hugely diverse populations of viruses. Eukaryotic microalgae form a ubiquitous and particularly dynamic fraction of such plankton, with environmental clone libraries from coastal regions sometimes being dominated by one or more of the three genera Bathycoccus, Micromonas, and Ostreococcus (class Prasinophyceae). The complete sequences of two double-stranded (dsDNA) Bathycoccus, one dsDNA Micromonas, and one new dsDNA Ostreococcus virus genomes are described. Genome comparison of these giant viruses revealed a high degree of conservation, both for orthologous genes and for synteny, except for one 36-kb inversion in the Ostreococcus lucimarinus virus and two very large predicted proteins in Bathycoccus prasinos viruses. These viruses encode a gene repertoire of certain amino acid biosynthesis pathways never previously observed in viruses that are likely to have been acquired from lateral gene transfer from their host or from bacteria. Pairwise comparisons of whole genomes using all coding sequences with homologous counterparts, either between viruses or between their corresponding hosts, revealed that the evolutionary divergences between viruses are lower than those between their hosts, suggesting either multiple recent host transfers or lower viral evolution rates.

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Hofstatter, Paulo G., Alexander K. Tice, Seungho Kang, Matthew W. Brown e Daniel J. G. Lahr. "Evolution of bacterial recombinase A ( recA ) in eukaryotes explained by addition of genomic data of key microbial lineages". Proceedings of the Royal Society B: Biological Sciences 283, n. 1840 (12 ottobre 2016): 20161453. http://dx.doi.org/10.1098/rspb.2016.1453.

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Recombinase enzymes promote DNA repair by homologous recombination. The genes that encode them are ancestral to life, occurring in all known dominions: viruses, Eubacteria, Archaea and Eukaryota. Bacterial recombinases are also present in viruses and eukaryotic groups (supergroups), presumably via ancestral events of lateral gene transfer. The eukaryotic recA genes have two distinct origins (mitochondrial and plastidial), whose acquisition by eukaryotes was possible via primary (bacteria–eukaryote) and/or secondary (eukaryote–eukaryote) endosymbiotic gene transfers (EGTs). Here we present a comprehensive phylogenetic analysis of the recA genealogy, with substantially increased taxonomic sampling in the bacteria, viruses, eukaryotes and a special focus on the key eukaryotic supergroup Amoebozoa, earlier represented only by Dictyostelium . We demonstrate that several major eukaryotic lineages have lost the bacterial recombinases (including Opisthokonta and Excavata), whereas others have retained them (Amoebozoa, Archaeplastida and the SAR-supergroups). When absent, the bacterial recA homologues may have been lost entirely (secondary loss of canonical mitochondria) or replaced by other eukaryotic recombinases. RecA proteins have a transit peptide for organellar import, where they act. The reconstruction of the RecA phylogeny with its EGT events presented here retells the intertwined evolutionary history of eukaryotes and bacteria, while further illuminating the events of endosymbiosis in eukaryotes by expanding the collection of widespread genes that provide insight to this deep history.

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Chen, Wen-Ming, Lionel Moulin, Cyril Bontemps, Peter Vandamme, Gilles Béna e Catherine Boivin-Masson. "Legume Symbiotic Nitrogen Fixation byβ-Proteobacteria Is Widespread inNature". Journal of Bacteriology 185, n. 24 (15 dicembre 2003): 7266–72. http://dx.doi.org/10.1128/jb.185.24.7266-7272.2003.

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ABSTRACT Following the initial discovery of two legume-nodulating Burkholderia strains (L. Moulin, A. Munive, B. Dreyfus, and C. Boivin-Masson, Nature 411:948-950, 2001), we identified as nitrogen-fixing legume symbionts at least 50 different strains of Burkholderia caribensis and Ralstonia taiwanensis, all belonging to the β-subclass of proteobacteria, thus extending the phylogenetic diversity of the rhizobia. R. taiwanensis was found to represent 93% of the Mimosa isolates in Taiwan, indicating thatβ -proteobacteria can be the specific symbionts of a legume. The nod genes of rhizobial β-proteobacteria (β-rhizobia) are very similar to those of rhizobia from theα -subclass (α-rhizobia), strongly supporting the hypothesis of the unique origin of common nod genes. Theβ -rhizobial nod genes are located on a 0.5-Mb plasmid, together with the nifH gene, in R. taiwanensis and Burkholderia phymatum. Phylogenetic analysis of available nodA gene sequences clustered β-rhizobial sequences in two nodA lineages intertwined with α-rhizobial sequences. On the other hand, theβ -rhizobia were grouped with free-living nitrogen-fixingβ -proteobacteria on the basis of the nifH phylogenetic tree. These findings suggest that β-rhizobia evolved from diazotrophs through multiple lateral nod gene transfers.

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Sorhannus, Ulf. "Evolution of Type II Antifreeze Protein Genes in Teleost Fish: A Complex Scenario Involving Lateral Gene Transfers and Episodic Directional Selection". Evolutionary Bioinformatics 8 (gennaio 2012): EBO.S9976. http://dx.doi.org/10.4137/ebo.s9976.

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Davies, Mark R., David J. McMillan, Gary H. Van Domselaar, Malcolm K. Jones e Kadaba S. Sriprakash. "Phage 3396 from a Streptococcus dysgalactiae subsp. equisimilis Pathovar May Have Its Origins in Streptococcus pyogenes". Journal of Bacteriology 189, n. 7 (26 gennaio 2007): 2646–52. http://dx.doi.org/10.1128/jb.01590-06.

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ABSTRACT Streptococcus dysgalactiae subsp. equisimilis strains (group G streptococcus [GGS]) are largely defined as commensal organisms, which are closely related to the well-defined human pathogen, the group A streptococcus (GAS). While lateral gene transfers are emerging as a common theme in these species, little is known about the mechanisms and role of these transfers and their effect on the population structure of streptococci in nature. It is now becoming evident that bacteriophages are major contributors to the genotypic diversity of GAS and, consequently, are pivotal to the GAS strain structure. Furthermore, bacteriophages are strongly associated with altering the pathogenic potential of GAS. In contrast, little is know about phages from GGS and their role in the population dynamics of GGS. In this study we report the first complete genome sequence of a GGS phage, Φ3396. Exhibiting high homology to the GAS phage Φ315.1, the chimeric nature of Φ3396 is unraveled to reveal evidence of extensive ongoing genetic diversity and dissemination of streptococcal phages in nature. Furthermore, we expand on our recent findings to identify inducible Φ3396 homologues in GAS from a region of endemicity for GAS and GGS infection. Together, these findings provide new insights into not only the population structure of GGS but also the overall population structure of the streptococcal genus and the emergence of pathogenic variants.

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Kenarkoohi, Azra, Amir Abdoli, Arman Rostamzad, Mahmoud Rashnavadi, Razi Naserifar, Jahangir Abdi, Morteza Shams et al. "Presence of CRISPR CAS-Like Sequences as a Proposed Mechanism for Horizontal Genetic Exchanges between Trichomonas vaginalis and Its Associated Virus: A Comparative Genomic Analysis with the First Report of a Putative CRISPR CAS Structures in Eukaryotic Cells". BioMed Research International 2023 (27 novembre 2023): 1–13. http://dx.doi.org/10.1155/2023/8069559.

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Introduction. Trichomonas vaginalis genome is among the largest genome size and coding capacities. Combinations of gene duplications, transposon, repeated sequences, and lateral gene transfers (LGTs) have contributed to the unexpected large genomic size and diversity. This study is aimed at investigating genomic exchange and seeking for presence of the CRISPR CAS system as one of the possible mechanisms for some level of genetic exchange. Material and Methods. In this comparative analysis, 398 publicly available Trichomonas vaginalis complete genomes were investigated for the presence of CRISPR CAS. Spacer sequences were also analyzed for their origin using BLAST. Results. We identified a CRISPR CAS (Cas3). CRISPR spacers are highly similar to transposable genetic elements such as viruses of protozoan parasites, especially megavirals, some transposons, and, interestingly, papillomavirus and HIV-1 in a few cases. Discussion. There is a striking similarity between the prokaryotes/Archaean CRISPR and what we find as eukaryotic CRISPR. About 5-10% of the 398 T. vaginalis possess a CRISPR structure. Conclusion. According to sequences and their organization, we assume that these repeated sequences and spacer, along with their mentioned features, could be the eukaryotic homolog of prokaryotes and Archaean CRISPR systems and may involve in a process similar to the CRISPR function.

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Coombs, J. M., e T. Barkay. "New Findings on Evolution of Metal Homeostasis Genes: Evidence from Comparative Genome Analysis of Bacteria and Archaea". Applied and Environmental Microbiology 71, n. 11 (novembre 2005): 7083–91. http://dx.doi.org/10.1128/aem.71.11.7083-7091.2005.

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ABSTRACT In order to examine the natural history of metal homeostasis genes in prokaryotes, open reading frames with homology to characterized PIB-type ATPases from the genomes of 188 bacteria and 22 archaea were investigated. Major findings were as follows. First, a high diversity in N-terminal metal binding motifs was observed. These motifs were distributed throughout bacterial and archaeal lineages, suggesting multiple loss and acquisition events. Second, the CopA locus separated into two distinct phylogenetic clusters, CopA1, which contained ATPases with documented Cu(I) influx activity, and CopA2, which contained both efflux and influx transporters and spanned the entire diversity of the bacterial domain, suggesting that CopA2 is the ancestral locus. Finally, phylogentic incongruences between 16S rRNA and PIB-type ATPase gene trees identified at least 14 instances of lateral gene transfer (LGT) that had occurred among diverse microbes. Results from bootstrapped supported nodes indicated that (i) a majority of the transfers occurred among proteobacteria, most likely due to the phylogenetic relatedness of these organisms, and (ii) gram-positive bacteria with low moles percent G+C were often involved in instances of LGT. These results, together with our earlier work on the occurrence of LGT in subsurface bacteria (J. M. Coombs and T. Barkay, Appl. Environ. Microbiol. 70:1698-1707, 2004), indicate that LGT has had a minor role in the evolution of PIB-type ATPases, unlike other genes that specify survival in metal-stressed environments. This study demonstrates how examination of a specific locus across microbial genomes can contribute to the understanding of phenotypes that are critical to the interactions of microbes with their environment.

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Dvornyk, Volodymyr. "Evolution of the Circadian Clock Mechanism in Prokaryotes". Israel Journal of Ecology and Evolution 52, n. 3-4 (12 aprile 2006): 343–57. http://dx.doi.org/10.1560/ijee_52_3-4_343.

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The circadian system of prokaryotes is probably the oldest among the circadian systems of living organisms. The genes comprising the system are very different in their evolutionary histories. The reconstruction of macroevolution of the circadian genes in cyanobacteria suggests that there are probably at least two types of circadian systems, based either on the threekaigenes (kaiA, kaiB, andkaiC) or onkaiBandkaiC.When referred to the recently published results about a genomic timescale of prokaryote evolution, the origin ofkaiBandsasAcorresponds to the appearance of anoxygenic photosynthesis, while the origin of thekaiBCoperon corresponds to the time when oxygenic photosynthesis evolved.The results of the studies performed so far suggest that major steps in macroevolution of the circadian system in cyanobacteria have been related to global changes in the environment and to keystone advances in biological evolution. This macroevolution has involved selection, multiple lateral transfers, gene duplications, and fusions as its primary driving forces. The proposed scenario of the circadian system's macroevolution is far from complete and will be updated as new genomic and sequence data are accumulated.

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LAM, WINNIE W. M., KEITH C. C. CHAN, DAVID K. Y. CHIU e ANDREW K. C. WONG. "A GRAPH-BASED ALGORITHM FOR MINING MULTI-LEVEL PATTERNS IN GENOMIC DATA". Journal of Bioinformatics and Computational Biology 08, n. 05 (ottobre 2010): 789–807. http://dx.doi.org/10.1142/s0219720010005002.

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Comparative genomics is concerned with the study of genome structure and function of different species. It can provide useful information for the derivation of evolutionary and functional relationships between genomes. Previous work on genome comparison focuses mainly on comparing the entire genomes for visualization without further analysis. As many interesting patterns may exist between genomes and may lead to the discovering of functional gene segments (groups of genes), we propose an algorithm called Multi-Level Genome Comparison Algorithm (MGC) that can be used to facilitate the analysis of genomes at multi-levels during the comparison process to discover sequential and regional consistency in gene segments. Different genomes may have common sub-sequences that differ from each other due to mutations, lateral gene transfers, gene rearrangements, etc., and these sub-sequences are usually not easily identified. Not all the genes can have a perfect one-to-one matching with each other. It is quite possible for one-to-many or many-to-many ambiguous relationships to exist between them. To perform the tasks effectively, MGC takes such ambiguity into consideration during genome comparison by representing genomes in a graph and then make use of a graph mining algorithm called the Multi-Level Attributed Graph Mining Algorithm (MAGMA) to build a hierarchical multi-level graph structure to facilitate genome comparison. To determine the effectiveness of these proposed algorithms, experiments were performed using intra- and inter-species of Microbial genomes. The results show that the proposed algorithms are able to discover multiple level matching patterns that show the similarities and dissimilarities among different genomes, in addition to confirming the specific role of the genes in the genomes.

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Liu, Yuchen, Robert H. White e William B. Whitman. "Methanococci Use the Diaminopimelate Aminotransferase (DapL) Pathway for Lysine Biosynthesis". Journal of Bacteriology 192, n. 13 (23 aprile 2010): 3304–10. http://dx.doi.org/10.1128/jb.00172-10.

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ABSTRACT The pathway of lysine biosynthesis in the methanococci has not been identified previously. A variant of the diaminopimelic acid (DAP) pathway uses diaminopimelate aminotransferase (DapL) to catalyze the direct conversion of tetrahydrodipicolinate (THDPA) to ll-DAP. Recently, the enzyme DapL (MTH52) was identified in Methanothermobacter thermautotrophicus and shown to belong to the DapL1 group. Although the Methanococcus maripaludis genome lacks a gene that can be unambiguously assigned a DapL function based on sequence similarity, the open reading frame MMP1527 product shares 30% amino acid sequence identity with MTH52. A Δmmp1527 deletion mutant was constructed and found to be a lysine auxotroph, suggesting that this DapL homolog in methanococci is required for lysine biosynthesis. In cell extracts of the M. maripaludis wild-type strain, the specific activity of DapL using ll-DAP and α-ketoglutarate as substrates was 24.3 ± 2.0 nmol min−1 mg of protein−1. The gene encoding the DapL homolog in Methanocaldococcus jannaschii (MJ1391) was cloned and expressed in Escherichia coli, and the protein was purified. The maximum activity of MJ1391 was observed at 70°C and pH 8.0 to 9.0. The apparent Km s of MJ1391 for ll-DAP and α-ketoglutarate were 82.8 ± 10 μM and 0.42 ± 0.02 mM, respectively. MJ1391 was not able to use succinyl-DAP or acetyl-DAP as a substrate. Phylogenetic analyses suggested that two lateral gene transfers occurred in the DapL genes, one from the archaea to the bacteria in the DapL2 group and one from the bacteria to the archaea in the DapL1 group. These results demonstrated that the DapL pathway is present in marine methanogens belonging to the Methanococcales.

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Falkowski, Paul G., e Linda V. Godfrey. "Electrons, life and the evolution of Earth's oxygen cycle". Philosophical Transactions of the Royal Society B: Biological Sciences 363, n. 1504 (16 maggio 2008): 2705–16. http://dx.doi.org/10.1098/rstb.2008.0054.

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The biogeochemical cycles of H, C, N, O and S are coupled via biologically catalysed electron transfer (redox) reactions. The metabolic processes responsible for maintaining these cycles evolved over the first ca 2.3 Ga of Earth's history in prokaryotes and, through a sequence of events, led to the production of oxygen via the photobiologically catalysed oxidation of water. However, geochemical evidence suggests that there was a delay of several hundred million years before oxygen accumulated in Earth's atmosphere related to changes in the burial efficiency of organic matter and fundamental alterations in the nitrogen cycle. In the latter case, the presence of free molecular oxygen allowed ammonium to be oxidized to nitrate and subsequently denitrified. The interaction between the oxygen and nitrogen cycles in particular led to a negative feedback, in which increased production of oxygen led to decreased fixed inorganic nitrogen in the oceans. This feedback, which is supported by isotopic analyses of fixed nitrogen in sedimentary rocks from the Late Archaean, continues to the present. However, once sufficient oxygen accumulated in Earth's atmosphere to allow nitrification to out-compete denitrification, a new stable electron ‘market’ emerged in which oxygenic photosynthesis and aerobic respiration ultimately spread via endosymbiotic events and massive lateral gene transfer to eukaryotic host cells, allowing the evolution of complex (i.e. animal) life forms. The resulting network of electron transfers led a gas composition of Earth's atmosphere that is far from thermodynamic equilibrium (i.e. it is an emergent property), yet is relatively stable on geological time scales. The early coevolution of the C, N and O cycles, and the resulting non-equilibrium gaseous by-products can be used as a guide to search for the presence of life on terrestrial planets outside of our Solar System.

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Zhaxybayeva, Olga, e W. Ford Doolittle. "Lateral gene transfer". Current Biology 21, n. 7 (aprile 2011): R242—R246. http://dx.doi.org/10.1016/j.cub.2011.01.045.

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