Abstract:
BACKGROUND:Bacterial global regulators each regulate the expression of several hundred genes. In Escherichia coli, the top seven global regulators together control over half of all genes. Leucine-responsive regulatory protein (Lrp) is one of these top seven global regulators. Lrp orthologs are very widely distributed, among both Bacteria and Archaea. Surprisingly, even within the phylum γ-Proteobacteria (which includes E. coli), Lrp is a global regulator in some orders and a local regulator in others. This raises questions about the evolution of Lrp and, more broadly, of global regulators. RESULTS:We examined Lrp sequences from four bacterial orders of the γ-Proteobacteria using phylogenetic and Logo analyses. The orders studied were Enterobacteriales and Vibrionales, in which Lrp plays a global role in tested species; Pasteurellales, in which Lrp is a local regulator in the tested species; and Alteromonadales, an order closely related to the other three but in which Lrp has not yet been studied. For comparison, we analyzed the Lrp paralog AsnC, which in all tested cases is a local regulator. The Lrp and AsnC phylogenetic clusters each divided, as expected, into subclusters representing the Enterobacteriales, Vibrionales, and Pasteuralles. However the Alteromonadales did not yield coherent clusters for either Lrp or AsnC. Logo analysis revealed signatures associated with globally- vs. locally- acting Lrp orthologs, providing testable hypotheses for which portions of Lrp are responsible for a global vs. local role. These candidate regions include both ends of the Lrp polypeptide but not, interestingly, the highly-conserved helix-turn-helix motif responsible for DNA sequence specificity. CONCLUSIONS:Lrp and AsnC have conserved sequence signatures that allow their unambiguous annotation, at least in γ-Proteobacteria. Among Lrp orthologs, specific residues correlated with global vs. local regulatory roles, and can now be tested to determine which are functionally relevant and which simply reflect divergence. In the Alteromonadales, it appears that there are different subgroups of Lrp orthologs, one of which may act globally while the other may act locally. These results suggest experiments to improve our understanding of the evolution of bacterial global regulators.
journal_name
BMC Evol Bioljournal_title
BMC evolutionary biologyauthors
Unoarumhi Y,Blumenthal RM,Matson JSdoi
10.1186/s12862-016-0685-1subject
Has Abstractpub_date
2016-05-20 00:00:00pages
111issue
1issn
1471-2148pii
10.1186/s12862-016-0685-1journal_volume
16pub_type
杂志文章abstract:BACKGROUND:Long-term monitoring of the biological impacts of the radioactive pollution caused by the Fukushima nuclear accident in March 2011 is required to understand what has occurred in organisms living in the polluted areas. Here, we investigated spatial and temporal changes of the abnormality rate (AR) in both fie...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-015-0297-1
更新日期:2015-02-10 00:00:00
abstract:BACKGROUND:A widely-used approach for screening nuclear DNA markers is to obtain sequence data and use bioinformatic algorithms to estimate which two alleles are present in heterozygous individuals. It is common practice to omit unresolved genotypes from downstream analyses, but the implications of this have not been i...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-10-118
更新日期:2010-04-30 00:00:00
abstract:BACKGROUND:In the large angiosperm order Lamiales, a diverse array of highly specialized life strategies such as carnivory, parasitism, epiphytism, and desiccation tolerance occur, and some lineages possess drastically accelerated DNA substitutional rates or miniaturized genomes. However, understanding the evolution of...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-10-352
更新日期:2010-11-12 00:00:00
abstract:BACKGROUND:Evolutionary transitions from terrestrial to aquatic life history cause drastic changes in sensory systems. Indeed, the drastic changes in vision have been reported in many aquatic amniotes, convergently. Recently, the opsin genes of the full-aquatic sea snakes have been reported. However, those of the amphi...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-020-01725-1
更新日期:2020-11-26 00:00:00
abstract:BACKGROUND:The mycobacterial genome is inclined to polymerase slippage and a high mutation rate in microsatellite regions due to high GC content and absence of a mismatch repair system. However, the exact molecular mechanisms underlying microsatellite variation have not been fully elucidated. Here, we investigated muta...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-11-247
更新日期:2011-08-31 00:00:00
abstract:BACKGROUND:Retrotransposons have been suggested to provide a substrate for non-allelic homologous recombination (NAHR) and thereby promote gene family expansion. Their precise role, however, is controversial. Here we ask whether retrotransposons contributed to the recent expansions of the Androgen-binding protein (Abp)...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-13-107
更新日期:2013-05-29 00:00:00
abstract:BACKGROUND:Cyanobacteria are photoautotrophic prokaryotes with wide variations in genome sizes and ecological habitats. Peroxiredoxin (PRX) is an important protein that plays essential roles in protecting own cells against reactive oxygen species (ROS). PRXs have been identified from mammals, fungi and higher plants. H...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-12-220
更新日期:2012-11-16 00:00:00
abstract:BACKGROUND:Chordate evolution is a history of innovations that is marked by physical and behavioral specializations, which led to the development of a variety of forms from a single ancestral group. Among other important characteristics, vertebrates obtained a well developed brain, anterior sensory structures, a closed...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-11-234
更新日期:2011-08-09 00:00:00
abstract:BACKGROUND:Although most insect species are specialized on one or few groups of plants, there are phytophagous insects that seem to use virtually any kind of plant as food. Understanding the nature of this ability to feed on a wide repertoire of plants is crucial for the control of pest species and for the elucidation ...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-016-0627-y
更新日期:2016-03-08 00:00:00
abstract:BACKGROUND:Publication of the first diatom genome, that of Thalassiosira pseudonana, established it as a model species for experimental and genomic studies of diatoms. Virtually every ensuing study has treated T. pseudonana as a marine diatom, with genomic and experimental data valued for their insights into the ecolog...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-11-125
更新日期:2011-05-14 00:00:00
abstract:BACKGROUND:The discovery of restriction endonucleases and modification DNA methyltransferases, key instruments of genetic engineering, opened a new era of molecular biology through development of the recombinant DNA technology. Today, the number of potential proteins assigned to type II restriction enzymes alone is bey...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-11-35
更新日期:2011-02-03 00:00:00
abstract:BACKGROUND:Lepidosauria (lizards, snakes, tuatara) is a globally distributed and ecologically important group of over 9,000 reptile species. The earliest fossil records are currently restricted to the Late Triassic and often dated to 227 million years ago (Mya). As these early records include taxa that are relatively d...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-13-208
更新日期:2013-09-25 00:00:00
abstract:BACKGROUND:Interspecies animal hybrids can employ clonal or hemiclonal reproduction modes where one or all parental genomes are transmitted to the progeny without recombination. Nevertheless, some interspecies hybrids retain strong connection with the parental species needed for successful reproduction. Appearance of p...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-017-1063-3
更新日期:2017-10-17 00:00:00
abstract:BACKGROUND:Patterns of genetic diversity between and within natural plant populations and their driving forces are of great interest in evolutionary biology. However, few studies have been performed on the genetic structure and population divergence in wild emmer wheat using a large number of EST-related single nucleot...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-13-169
更新日期:2013-08-13 00:00:00
abstract:BACKGROUND:Selective pressure from pathogens is thought to shape the allelic diversity of major histocompatibility complex (MHC) genes in vertebrates. In particular, both local adaptation to pathogens and gene flow are thought to explain a large part of the intraspecific variation observed in MHC allelic diversity. To ...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-017-0905-3
更新日期:2017-02-20 00:00:00
abstract:BACKGROUND:The classification of royal ferns (Osmundaceae) has long remained controversial. Recent molecular phylogenies indicate that Osmunda is paraphyletic and needs to be separated into Osmundastrum and Osmunda s.str. Here, however, we describe an exquisitely preserved Jurassic Osmunda rhizome (O. pulchella sp. nov...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-015-0400-7
更新日期:2015-06-30 00:00:00
abstract:BACKGROUND:Antarctic notothenioids are an impressive adaptive radiation. While they share recent common ancestry with several species-depauperate lineages that exhibit a relictual distribution in areas peripheral to the Southern Ocean, an understanding of their evolutionary origins and biogeographic history is limited ...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-015-0362-9
更新日期:2015-06-11 00:00:00
abstract:BACKGROUND:: Duplicated genes are common in vertebrate genomes. Their persistence is assumed to be either a consequence of gain of novel function (neofunctionalisation) or partitioning of the function of the ancestral molecule (sub-functionalisation). Surprisingly few studies have evaluated the extent of such modificat...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-7-221
更新日期:2007-11-12 00:00:00
abstract:BACKGROUND:While the pathogenesis and epidemiology of tuberculosis are well studied, relatively little is known about the evolution of the infectious agent Mycobacterium tuberculosis, especially at the within-host level. The insertion sequence IS6110 is a genetic marker that is widely used to track the transmission of ...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-4-31
更新日期:2004-09-09 00:00:00
abstract:BACKGROUND:Considerable attention has focused on how selection on dispersal and other core life-history strategies (reproductive effort, survival ability, colonization capacity) may lead to so-called dispersal syndromes. Studies on genetic variation in these syndromes within species could importantly increase our under...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-7-133
更新日期:2007-08-06 00:00:00
abstract:BACKGROUND:Understanding the evolution of species limits is important in ecology, evolution, and conservation biology. Despite its likely importance in the evolution of these limits, little is known about phenotypic covariance in geographically marginal populations, and the degree to which it constrains, or facilitates...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-13-105
更新日期:2013-05-28 00:00:00
abstract:BACKGROUND:Teleost radiation in the oceans required specific physiological adaptations in eggs and early embryos to survive in the hyper-osmotic seawater. Investigating the evolution of aquaporins (AQPs) in these vertebrates should help to elucidate how mechanisms for water homeostasis evolved. The marine teleost gilth...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-8-259
更新日期:2008-09-23 00:00:00
abstract:BACKGROUND:Past events like fluctuations in population size and post-glacial colonization processes may influence the relative importance of genetic drift, migration and selection when determining the present day patterns of genetic variation. We disentangle how drift, selection and migration shape neutral and adaptive...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-017-1022-z
更新日期:2017-08-14 00:00:00
abstract:BACKGROUND:Recent publications concerning the interordinal phylogeny of placental mammals have converged on a common signal, consisting of four major radiations with some ambiguity regarding the placental root. The DNA data with which these relationships have been reconstructed are easily accessible from public databas...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-7-108
更新日期:2007-07-03 00:00:00
abstract:BACKGROUND:Gene duplication has been identified as a key process driving functional change in many genomes. Several biological models exist for the evolution of a pair of duplicates after a duplication event, and it is believed that gene duplicates can evolve in different ways, according to one process, or a mix of pro...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-016-0848-0
更新日期:2017-01-31 00:00:00
abstract:BACKGROUND:The bananaquit (Coereba flaveola) is a small nectivorous and frugivorous emberizine bird (order Passeriformes) that is an abundant resident throughout the Caribbean region. We used multi-gene analyses to investigate the evolutionary history of this species throughout its distribution in the West Indies and i...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-8-240
更新日期:2008-08-22 00:00:00
abstract:BACKGROUND:The Visayan Tarictic Hornbill (Penelopides panini) and the Walden's Hornbill (Aceros waldeni) are two threatened hornbill species endemic to the western islands of the Visayas that constitute - between Luzon and Mindanao - the central island group of the Philippine archipelago. In order to evaluate their gen...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-12-203
更新日期:2012-10-12 00:00:00
abstract:BACKGROUND:The genus Corbicula is one of the most invasive groups of molluscs. It includes both sexual and androgenetic lineages. The present study re-assessed the different morphotypes and haplotypes of West European Corbicula in order to clarify their taxonomic identification and phylogenetic relationships with Ameri...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-11-147
更新日期:2011-05-27 00:00:00
abstract:BACKGROUND:The Pomatiopsidae are reported from northern India into southern China and Southeast Asia, with two sub-families, the Pomatiopsinae (which include freshwater, amphibious, terrestrial and marine species) and the freshwater Triculinae. Both include species acting as intermediate host for species of the blood-f...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-14-29
更新日期:2014-02-18 00:00:00
abstract:BACKGROUND:Speciation often occurs in complex or uncertain temporal and spatial contexts. Processes such as reinforcement, allopatric divergence, and assortative mating can proceed at different rates and with different strengths as populations diverge. The Central American Midas cichlid fish species complex is an impor...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-7-25
更新日期:2007-02-20 00:00:00