Specific Clades Research Articles

Sequence and functional analysis of cis-elements associated with MIR159 loci from Brassica juncea reveal functional diversification and complex transcriptional regulation

Identification and functional analysis of promoters is critical towards gaining insights into transcriptional regulation, and helps in identifying interacting trans-factors. Analysis of MIRNA promoter can differentiate the function of paralogs and homeologs where identifying the role of members of MIRNA family is difficult based on small RNA blots due to near-identical mature sequences. The role of miRNA as regulators of development and adaptation in polyploid species-Brassica, and the impact of polyploidy on divergence among paralogs and homeologs especially with reference to transcriptional regulation remains unexplored. We identified homologs of MIR159 from 137 species across plants based on their homology to pre-MIR159A, MIR159B, and MIR159C from Arabidopsis and retrieved their promoter sequences. Promoter sequence analysis revealed high level of divergence; albeit clades of closely related taxonomic units were obtained. We detected biased, but no lineage-specific distribution of transcription factor binding motifs (TFBS) in families. Phylogenetic reconstruction in Brassicaceae revealed genome- and sub-genome specific clades. We isolated three homeologs of MIR159A, and one of MIR159C from the A-genome of B. juncea. Functional characterization involved transgenic lines in A. thaliana Col-0 with promoter::reporter transcriptional fusions (p-MIR159::GUS::ter) and monitoring of reporter activity during development, abiotic stresses, and after administering hormones. Comparison of reporter activity of full-length promoters across homeologs and paralogs reveal extensive functional diversification. Comparative analysis of reporter activity of nested deletions, and with distribution of TFBS did not yield a clear correlation. In summary, analysis of GUS during development, hormone treatment and abiotic stresses reveal complex transcriptional regulation of MIR159 expression.

Expansin gene loss is a common occurrence during adaptation to an aquatic environment.

Expansins comprise a superfamily of plant cell wall loosening proteins that can be divided into four individual families (EXPA, EXPB, EXLA and EXLB). Aside from inferred roles in a variety of plant growth and developmental traits, little is known regarding the function of specific expansin clades, for which there are at least 16 in flowering plants (angiosperms); however, there is evidence to suggest that some expansins have cell-specific functions, in root hair and pollen tube development, for example. Recently, two duckweed genomes have been sequenced (Spirodela polyrhiza strains 7498 and 9509), revealing significantly reduced superfamily sizes. We hypothesized that there would be a correlation between expansin loss and morphological reductions seen among highly adapted aquatic species. In order to provide an answer to this question, we characterized the expansin superfamilies of the greater duckweed Spirodela, the marine eelgrass Zostera marina and the bladderwort Utricularia gibba. We discovered rampant expansin gene and clade loss among the three, including a complete absence of the EXLB family and EXPA-VII. The most convincing correlation between morphological reduction and expansin loss was seen for Utricularia and Spirodela, which both lack root hairs and the root hair expansin clade EXPA-X. Contrary to the pattern observed in other species, four Utricularia expansins failed to branch within any clade, suggesting that they may be the result of neofunctionalization. Last, an expansin clade previously discovered only in eudicots was identified in Spirodela, allowing us to conclude that the last common ancestor of monocots and eudicots contained a minimum of 17 expansins.

A novel avian isolate of hepatitis E virus from Pakistan

BackgroundAvian hepatitis E virus (aHEV) has been associated with hepatitis-splenomegaly syndrome (HSS) in chickens along with asymptomatic subclinical infection in many cases. So far, four genotypes have been described, which cause infection in chickens, specifically in broiler breeders and layer chickens. In the present study, we isolated and identified two novel aHEV strains from the bile of layer chickens in Pakistan evincing clinical symptoms related to HSS.MethodologyHistology of liver and spleen tissues was carried out to observe histopathological changes in these tissues. Bile fluid and fecal suspensions were used for viral RNA isolation through MegNA pure and Trizol method which was further used for viral genome detection and characterization by cDNA synthesis and amplification of partial open reading frame (ORF) 1, ORF2 and complete ORF3. The bioinformatics tools; Molecular Evolutionary Genetics Analysis version 6.0 (MEGA 6), Mfold and ProtScale were used for phylogenic analysis, RNA secondary structure prediction and protein hydropathy analysis, respectively.ResultsSequencing and phylogenetic analysis on the basis of partial methyltranferase (MeT), helicase (Hel) domain, ORF2 and complete ORF3 sequence suggests these Pakistani aHEV (Pak aHEV) isolates may belong to a Pakistani specific clade. The overall sequence similarity between the Pak aHEV sequences was 98–100%. The ORF1/ORF3 intergenic region contains a conserved cis-reactive element (CRE) and stem-loop structure (SLS). Analysis of the amino acid sequence of ORF3 indicated two hydrophobic domains (HD) and single conserved proline-rich domain (PRD) PREPSAPP (PXXPXXPP) with a single PSAP motif found in C-terminal. Amino acid changes S15 T, A31T, Q35H and G46D unique to the Pak aHEV sequences were found in the N-terminal region of ORF3.ConclusionsOur data suggests that Pak aHEV isolates may represent a novel Pakistani clade and high sequence homology to each other support the supposition they may belong to a monophyletic clade circulating in the region around Pakistan. The data presented in this study provide further information for aHEV genetic diversity, genotype mapping, global distribution and epidemiology.

Phylogenetic distribution of the bacteriocin repertoire of lactic acid bacteria species associated with artisanal cheese

The microbiota contributes to artisanal cheese bioprotection and biopreservation through inter and intraspecific competition. This work aimed to investigate the phylogenetic distribution of the repertoire of bacteriocin structural genes of model lactic acid bacteria (LAB) in order to investigate its respective role in the artisanal cheeses microenvironment. A phylogenetic analysis of the rRNA 16S gene from 445 model strains of LAB was conducted using bayesian inference and the repertoire of bacteriocin genes was predicted from these strains by BAGEL software. Bacterial strains were clustered in five monophyletic clades (A, B, C, D and E) with high posterior probability values (PP > 0.99). One bacteriocin structural gene was predicted for 88.5% of the analyzed strains. The majority of the species encoded different classes of bacteriocins. Greater diversity of bacteriocin genes was found for strains included in clade A, comprising Lactococcus lactis, Streptococcus agalactiae, Streptococcus thermophilus, Streptococcus macedonicus, Enterococcus faecalis and Enterococcus faecium. In addition, Lactococcus lactis presented higher diversity of bacteriocin classes, encoding glycocins, lanthipeptides, sactipeptides, cyclic and linear azole-containing peptides, included in bacteriocins class I, besides class II and III. The results suggest that the distribution of bacteriocin structural genes is related to the phylogenetic clades of LAB species, with a higher frequency in some specific clades. Information comprised in this study contributes to comprehend the bacterial competition mechanisms in the artisanal cheese microenvironment.

The Strange Case of Prevotella copri: Dr. Jekyll or Mr. Hyde?

This issue of Cell Host & Microbe highlights the opposite faces of Prevotella copri (P.copri). Tett etal. (2019) and Fehlner-Peach etal. (2019) unravel the complexity of gut dwelling P.copri, whereas Rolhion etal. (2019) explore the P.copri dark side with its ability to potentiate Listeria monocytogenes pathogenicity.

Sexual Selection and the Evolution of Male Reproductive Traits in Benthic Octopuses.

Competition between same-sex organisms, or intra-sexual selection, can occur before and after mating, and include processes such as sperm competition and cryptic female choice. One of the consequences of intra-sexual selection is that male reproductive traits tend to evolve and diverge at high rates. In benthic octopuses, females often mate with more than one male in a single reproductive event, opening the venue for intra-sexual selection at multiple levels. For instance, males transfer spermatophores through hectocotylus, and can remove the spermatophores left by other males. Considering the limited evidence on post-copula competition in benthic octopuses, and the potential to affect the evolution of reproductive traits within octopodids, we put this hypothesis to a test employing a phylogenetic comparative approach. We combined data on hectocotylized arm length (HAL), ligula length (LL), spermatophore length (SL) with a Bayesian molecular phylogeny of 87 species, to analyze how reproductive traits have diverged across lineages and covary with body size (mantle length; ML). First, additionally to ML, we estimated the phylogenetic signal (λ) and mode of evolution (κ) in each reproductive trait. Second, we performed phylogenetic regressions to quantify the association among reproductive traits and their co-variation with ML. This analysis allowed us to estimate the phenotypic change along a branch into the phylogeny, and whether selection may have played a role in the evolution and diversification of specific clades. Estimations of λ were always high (>0.75), indicating concordance between the traits and the topology of the phylogenetic tree. Low values of κ (<1.0) suggested that evolution depends on branch lengths. All reproductive traits exhibiting a positive relation with ML (β > 0.5 in all cases). Overall, evolutionary rate models applied to the SL-ML regression suggested that octopuses of the family Megaleledonidae have evolved larger spermatophores than expected for their size. The regression HAL-ML indicated that HAL was more variable in Megaleledonidae than in the remaining clades, suggesting that the high divergence across species within this group might partially reflect intra-sexual selection. These results support the hypothesis that, at least in some lineages, sexual selection may account for the divergence in reproductive traits of male octopuses.

Interrogating Genomic-Scale Data for Squamata (Lizards, Snakes, and Amphisbaenians) Shows no Support for Key Traditional Morphological Relationships.

Genomics is narrowing uncertainty in the phylogenetic structure for many amniote groups. For one of the most diverse and species-rich groups, the squamate reptiles (lizards, snakes, and amphisbaenians), an inverse correlation between the number of taxa and loci sampled still persists across all publications using DNA sequence data and reaching a consensus on the relationships among them has been highly problematic. In this study, we use high-throughput sequence data from 289 samples covering 75 families of squamates to address phylogenetic affinities, estimate divergence times, and characterize residual topological uncertainty in the presence of genome-scale data. Importantly, we address genomic support for the traditional taxonomic groupings Scleroglossa and Macrostomata using novel machine-learning techniques. We interrogate genes using various metrics inherent to these loci, including parsimony-informative sites (PIS), phylogenetic informativeness, length, gaps, number of substitutions, and site concordance to understand why certain loci fail to find previously well-supported molecular clades and how they fail to support species-tree estimates. We show that both incomplete lineage sorting and poor gene-tree estimation (due to a few undesirable gene properties, such as an insufficient number of PIS), may account for most gene and species-tree discordance. We find overwhelming signal for Toxicofera, and also show that none of the loci included in this study supports Scleroglossa or Macrostomata. We comment on the origins and diversification of Squamata throughout the Mesozoic and underscore remaining uncertainties that persist in both deeper parts of the tree (e.g., relationships between Dibamia, Gekkota, and remaining squamates; among the three toxicoferan clades Iguania, Serpentes, and Anguiformes) and within specific clades (e.g., affinities among gekkotan, pleurodont iguanians, and colubroid families).

Gardnerella vaginalis Clade Distribution Is Associated With Behavioral Practices and Nugent Score in Women Who Have Sex With Women.

Gardnerella vaginalis is detected in women with and without bacterial vaginosis (BV). Identification of 4 G. vaginalis clades raised the possibility that pathogenic and commensal clades exist. We investigated the association of behavioral practices and Nugent Score with G. vaginalis clade distribution in women who have sex with women (WSW). Longitudinal self-collected vaginal specimens were analyzed using established G. vaginalis species-specific and clade-typing polymerase chain reaction assays. Logistic regression assessed factors associated with detection of G. vaginalis clades, and multinomial regression assessed factors associated with number of clades. Clades 1, 2, and 3 and multiclade communities (<2 clades) were associated with Nugent-BV. Clade 1 (odds ratio [OR], 3.36; 95% confidence interval [CI], 1.65-6.84) and multiclade communities (relative risk ratio [RRR], 9.51; 95% CI, 4.36-20.73) were also associated with Lactobacillus-deficient vaginal microbiota. Clade 4 was neither associated with Nugent-BV nor Lactobacillus-deficient microbiota (OR, 1.49; 95% CI, 0.67-3.33). Specific clades were associated with differing behavioral practices. Clade 1 was associated with increasing number of recent sexual partners and smoking, whereas clade 2 was associated with penile-vaginal sex and sharing of sex toys with female partners. Our results suggest that G. vaginalis clades have varying levels of pathogenicity in WSW, with acquisition occurring through sexual activity. These findings suggest that partner treatment may be an appropriate strategy to improve BV cure.

A novel taxon selection method, aimed at minimizing recombination, clarifies the discovery of a new sub-population of Helicobacter pylori from Australia.

We present a novel method for taxon selection, the aim being to minimize problems arising from highly recombinant species such as Helicobacter pylori. Helicobacter pylori has accompanied modern‐human migration out of Africa and is marked by a phylogeographic strain distribution, which has been exploited to add an extra layer of information about human migrations to that obtained from human sources. However, H. pylori's genome has high sequence heterogeneity combined with a very high rate of recombination, causing major allelic diversification across strains. On the other hand, recombination events that have become preserved in sub‐populations are a useful source of phylogenetic information. This creates a potential problem in selecting representative strains for particular genetic or phylogeographic clusters and generally ameliorating the impact on analyses of extensive low‐level recombination. To address this issue, we perform multiple population structure‐based analyses on core genomes to select exemplar strains, called ‘quintessents’, which exhibit limited recombination. In essence, quintessent strains are representative of their specific phylogenetic clades and can be used to refine the current MLST concatenation‐based population structure classification system. The use of quintessents reduces the noise due to local recombination events, while preserving recombination events that have become fixed in sub‐populations. We illustrate the method with an analysis of core genome concatenations from 185 H. pylori strains, which reveals a recent speciation event resulting from the recombination of strains from phylogeographic clade hpSahul, carried by Aboriginal Australians, and hpEurope, carried by some of the people who arrived in Australia over the past 200 years. The signal is much clearer when based on quintessent strains, but absent from the analysis based on MLST concatenations.

Atlantic corals under climate change: modelling distribution shifts to predict richness, phylogenetic structure and trait-diversity changes

Climate change is altering species distributions worldwide. Particularly, global warming is driving range contractions and expansions of tropical species, such as corals. The use of climatic projections, via species distribution models to predict species distributional shifts, can identify threaten species and help to set priority areas of conservation. In this study, we assessed if distributional shifts of 45 Atlantic reef-forming corals (scleractinian), and the main environmental variables driving their distributions, correlated with their phylogeny and/or their functional traits; i.e. whether expected contractions and expansions affected specific clades, or specific coral traits. We also estimated the potential loss and/or gain of species richness, phylogenetic diversity (PD) and phylogenetic species variability (PSV), as well as the phylogenetic structure of Atlantic reef communities (‘clustering’, ‘overdispersion’ or ‘randomness’), under a future climate scenario (A2-IPCC-2100). The potential loss of Atlantic corals in the future will be randomly distributed across their phylogeny, i.e. potential extinctions will not only affect one section of the phylogeny, therefore alleviating an inordinate loss of evolutionary history. Nearly all current and future communities presented a ‘random’ phylogenetic structure. No correlation was found between distributional shifts and coral traits. Environmental variables did not show a significant correlation with the phylogeny neither with coral traits. Predicted changes in species richness, PD and PSV vary across the Atlantic; certain areas display large evolutionary diversity losses. Species belonging to isolated clades (high evolutionary distinctiveness) contribute to quantitative increases, or decreases, of PD and PSV, becoming crucial species for conservation. These findings highlight the importance of combining SDMs with phylogenetic/functional metrics to develop conservation strategies to assess the future of corals.

Effects of taxon sampling and tree reconstruction methods on phylodiversity metrics.

The amount and patterns of phylodiversity in a community are often used to draw inferences about the local and historical factors affecting community assembly and can be used to prioritize communities and locations for conservation. Because measures of phylodiversity are based on the topology and branch lengths of phylogenetic trees, which are affected by the number and diversity of taxa in the tree, these analyses may be sensitive to changes in taxon sampling and tree reconstruction methods.To investigate the effects of taxon sampling and tree reconstruction methods on measures of phylodiversity, we investigated the community phylogenetics of the Ordway‐Swisher Biological Station (Florida), which is home to over 600 species of vascular plants. We studied the effects of (a) the number of taxa included in the regional phylogeny; (b) random versus targeted sampling of species to assemble the regional species pool; (c) including only species from specific clades rather than broad sampling; (d) using trees reconstructed directly for the taxa under study compared to trees pruned from a larger reconstructed tree; and (e) using phylograms compared to chronograms.We found that including more taxa in a study increases the likelihood of observing significantly nonrandom phylogenetic patterns. However, there were no consistent trends in the phylodiversity patterns based on random taxon sampling compared to targeted sampling, or within individual clades compared to the complete dataset. Using pruned and reconstructed phylogenies resulted in similar patterns of phylodiversity, while chronograms in some cases led to significantly different results from phylograms.The methods commonly used in community phylogenetic studies can significantly impact the results, potentially influencing both inferences of community assembly and conservation decisions. We highlight the need for both careful selection of methods in community phylogenetic studies and appropriate interpretation of results, depending on the specific questions to be addressed.

From Intracellular Bacteria to Differentiated Bacteroids: Transcriptome and Metabolome Analysis in Aeschynomene Nodules Using the Bradyrhizobium sp. Strain ORS285 bclA Mutant.

Soil bacteria called rhizobia trigger the formation of root nodules on legume plants. The rhizobia infect these symbiotic organs and adopt an intracellular lifestyle within the nodule cells, where they differentiate into nitrogen-fixing bacteroids. Several legume lineages force their symbionts into an extreme cellular differentiation, comprising cell enlargement and genome endoreduplication. The antimicrobial peptide transporter BclA is a major determinant of this process in Bradyrhizobium sp. strain ORS285, a symbiont of Aeschynomene spp. In the absence of BclA, the bacteria proceed until the intracellular infection of nodule cells, but they cannot differentiate into enlarged polyploid and functional bacteroids. Thus, the bclA nodule bacteria constitute an intermediate stage between the free-living soil bacteria and the nitrogen-fixing bacteroids. Metabolomics on whole nodules of Aeschynomene afraspera and Aeschynomene indica infected with the wild type or the bclA mutant revealed 47 metabolites that differentially accumulated concomitantly with bacteroid differentiation. Bacterial transcriptome analysis of these nodules demonstrated that the intracellular settling of the rhizobia in the symbiotic nodule cells is accompanied by a first transcriptome switch involving several hundred upregulated and downregulated genes and a second switch accompanying the bacteroid differentiation, involving fewer genes but ones that are expressed to extremely elevated levels. The transcriptomes further suggested a dynamic role for oxygen and redox regulation of gene expression during nodule formation and a nonsymbiotic function of BclA. Together, our data uncover the metabolic and gene expression changes that accompany the transition from intracellular bacteria into differentiated nitrogen-fixing bacteroids.IMPORTANCE Legume-rhizobium symbiosis is a major ecological process, fueling the biogeochemical nitrogen cycle with reduced nitrogen. It also represents a promising strategy to reduce the use of chemical nitrogen fertilizers in agriculture, thereby improving its sustainability. This interaction leads to the intracellular accommodation of rhizobia within plant cells of symbiotic organs, where they differentiate into nitrogen-fixing bacteroids. In specific legume clades, this differentiation process requires the bacterial transporter BclA to counteract antimicrobial peptides produced by the host. Transcriptome analysis of Bradyrhizobium wild-type and bclA mutant bacteria in culture and in symbiosis with Aeschynomene host plants dissected the bacterial transcriptional response in distinct phases and highlighted functions of the transporter in the free-living stage of the bacterial life cycle.

Courtship Behavior and Advertisement Call Geographic Variation of Bokermannohyla luctuosa (Pombal Jr. and Haddad, 1993) (Hylidae, Cophomantini)

Reproduction is an important aspect of the natural history of anuran species; it includes, for example, selection of the calling site by males, mate attraction, courtship, oviposition, and subsequent parental care. Among these, courtship is one of the least studied phases of anuran reproductive biology. Therefore, we describe for the first time the complex courtship of Bokermannohyla luctuosa, which involves tactile communication and two types of vocalizations: advertisement and courtship calls. These calls have a pseudo-pulsed structure, with the courtship call being similar to the advertisement call but longer in duration and lower in dominant frequency and relative peak power. Most of the behavioral repertoire of B. luctuosa courtship matches that reported for other Cophomantini species. Additional information on the natural history of phylogenetic closely related species, besides improving autoecological knowledge, will enable the recognition of behavioral synapomorphies for specific clades.

The Apennines as a cryptic Pleistocene refugium of the bark beetle Pityogenes chalcographus (Coleoptera: Curculionidae).

The Apennine Mountains in Italy are an important biogeographical region and of particular interest in phylogeographical research, because they have been a refugium during Pleistocene glaciation events for numerous European species. We performed a genetic study on the Eurasian bark beetle Pityogenes chalcographus (Linnaeus, 1760), focusing on two Apennine (Italian) and two Central European (Austrian) locations to assess the influence of the Apennines in the evolutionary history of the beetle, particularly during the Pleistocene. We analysed a part of the mitochondrial COI gene and a set of 5470 informative genome-wide markers to understand its biogeography. We found 75 distinct mitochondrial haplotypes, which are structured in three main clades. In general, the Apennine locations harbour a higher number of mitochondrial clades than Central European sites, with one specific clade exclusively detected in the Apennines. Analysis of our genome-wide, multi-locus dataset reveals a clustering of P. chalcographus by geography, with Italian individuals clearly separated from Austrian samples. Our data highlight the significance of the Apennines for the genetic diversity of P. chalcographus and support the hypothesis that this area was an important refugium during unfavourable conditions in the Pleistocene. We discuss additional life-history traits and processes that shaped the evolution of this widespread beetle.

Phylogenetic signal in leaf-cutting ant diet in the fragmented Atlantic rain forest

AbstractLeaf-cutting ants are dominant herbivores in Neotropical rain forests, and their colony densities increase in disturbed habitats such as forest edges. However, while it is well-established that leaf-cutting ants profit from changes to the food-plant community, the phylogenetic dimension of this ant–plant interaction remains poorly understood in fragmented forests. We studied diet composition of Atta cephalotes in the edge and interior of Atlantic forest in north-east Brazil (8°30′S, 35°50′W). We applied phylogenetic signal analysis to investigate the diet across plant lineages and performed phylogenetic generalized linear models to analyse the diet in both habitats. We found a phylogenetic signal in diet and in leaf mechanical resistance, which means that A. cephalotes selects closely related food plants with less resistant leaves. Most preferred species belong to Malpighiales, Rubiaceae and Melastomataceae. We also found that irrespective of phylogeny, ants select food plants with less resistant leaves, both in edge and interior. However, ants choose more abundant plants only in edges. High abundance of optimal diet facilitates foraging in forest edges and explains why colony densities increase in disturbed habitats. Finally, by favouring or disfavouring specific clades, leaf-cutting ants contribute to changes in the phylogenetic structure of tropical rain forests, e.g. phylogenetic impoverishment.

Resolving the individual contribution of key microbial populations to enhanced biological phosphorus removal with Raman\u2013FISH

Enhanced biological phosphorus removal (EBPR) is a globally important biotechnological process and relies on the massive accumulation of phosphate within special microorganisms. Candidatus Accumulibacter conform to the classical physiology model for polyphosphate accumulating organisms and are widely believed to be the most important player for the process in full-scale EBPR systems. However, it was impossible till now to quantify the contribution of specific microbial clades to EBPR. In this study, we have developed a new tool to directly link the identity of microbial cells to the absolute quantification of intracellular poly-P and other polymers under in situ conditions, and applied it to eight full-scale EBPR plants. Besides Ca. Accumulibacter, members of the genus Tetrasphaera were found to be important microbes for P accumulation, and in six plants they were the most important. As these Tetrasphaera cells did not exhibit the classical phenotype of poly-P accumulating microbes, our entire understanding of the microbiology of the EBPR process has to be revised. Furthermore, our new single-cell approach can now also be applied to quantify storage polymer dynamics in individual populations in situ in other ecosystems and might become a valuable tool for many environmental microbiologists.

Characterization and expression profile analysis of YABBY family genes in Pak-choi (Brassica rapa ssp. chinensis) under abiotic stresses and hormone treatments

YABBY proteins are widely distributed among different plant species and exhibit a higher degree of prevalence in angiosperms than in gymnosperms; abaxial cell fate in the lateral organs of plants is mainly determined by the functions of YABBY genes. However, to date, no scientific study has been conducted on the functions and responses of these genes under different forms of abiotic stresses in Pak-choi (Brassica rapa ssp. chinensis). In this study, we cloned and identified 12 YABBY family genes from Pak-choi. The evolutionary history of the YABBY genes was studied in nine species and showed that YABBY gene loss occurred during specific periods or in certain species during evolution. The putative YABBY family genes of Pak-choi were comprehensively analyzed by comparison with the corresponding orthologs in Arabidopsis and Chinese cabbage (Brassica rapa ssp. pekinensis) and classified into five subfamilies based on the specific protein domains and phylogenetic clades. A subcellular localization assay involving BcYABBY1b and BcYABBY2c confirmed that the BcYABBY proteins were localized in the nucleus. qRT-PCR data revealed that the BcYABBY genes are specifically expressed in distinct organs and developmental stages. Furthermore, the expression profiles of the BcYABBY genes were investigated under different hormone treatments and abiotic stress factors. In this study, we comprehensively identified and analyzed the YABBY gene family in the Pak-choi genome. Our data provide possible functional information regarding the involvement of BcYABBY genes in plant growth and development and in the response to abiotic stress and hormone treatments.

Genetic diversity of multidrug-resistant Mycobacterium tuberculosis isolates in Punjab, Pakistan

Pakistan ranks 5th among the world's highest tuberculosis (TB) burden countries and 6th among the countries with the highest prevalence of drug-resistant TB. However, insufficient data are available on the genetic structure of M. tuberculosis strains circulating in this country. The objective of this study was to explore the genetic diversity of multidrug-resistant M. tuberculosis isolates from Punjab, Pakistan with a combination of spoligotyping and 24-loci MIRU-VNTR typing.Among a total of 127 MDR isolates studies, 53 spoligotypes were obtained, split into 14 clusters (n = 88, 69.3%, 2–29 isolates per cluster) and 39 (30.7%) unique patterns. At the phylogenetic level, the most prevalent sublineage was CAS1_DELHI (n = 53, 41.7%), mostly represented by ST 1942 (n = 29, 22.8%), followed by T1 (n = 14, 11%) and Beijing (n = 10, 7.8%). The remaining nine sublineages (CAS, MANU2, EAI5, T2, LAM10_CAM, H1, X1, H4 and CAS2) involved altogether 24 (18.9%) isolates. Twenty-six (20.5%) isolates could not be assigned to any specific clade. MIRU-VNTR typing identified 123 (96.8%), 97 (76.4%) and 65 (51.2%) unique types with a tolerance of 0, 1, and 2 locus differences between the patterns.Upon combined spoligotyping and MIRU-VNTR typing analysis, 123 (96.8%), 108 (85%), and 91 (71.7%) unique types were identified if a tolerance of 0, 1, and 2 locus differences in the MIRU-VNTR patterns was assumed, respectively. Based on the clustering results, the transmission rate for MDR-TB cases under the study was calculated at 3.2%, 15%, and 28.3%.Overall, three clades, namely CAS1_DELHI, T1, and Beijing accounted for the majority of MDR-TB cases in Pakistan. Up to a third of the cases were clustered upon combined spoligotyping and MIRU-VNTR typing, suggesting a moderate level of active transmission.

Shift in Bacillus sp. JR3 esterase LipJ activity profile after addition of essential residues from family I.5 thermophilic lipases

We recently described LipJ, a mesophilic esterase clustering in a specific clade of bacterial lipase family I.5, bearing the same structure but several distinct sequence motifs. Two mutagenesis approaches were used here to modify LipJ by addition of common features of family 1.5 lipases, searching for changes on the activity profile. Iterative saturation mutagenesis of a residue possibly involved in Zn2+ coordination produced a LipJ variant –H110N– displaying a remarkable shift in substrate specificity, possibly boosted by changes in number and distance of relevant polar interactions for Zn2+ coordination. Also, variants E27 A, G136 A and M139Q were obtained by site directed mutagenesis as single, double or triple mutants, showing a general shift in specificity towards higher temperature and longer chain-length substrates, all of them displaying higher activity than LipJ on C7 substrates. The results obtained suggest that the N-terminal region of LipJ may indeed contribute to substrate accommodation, whereas mutations at the pentapeptide displayed maximum activity at 50 °C, with the triple mutant showing activity even at 80 °C, greatly enhanced by Mn2+. 3D modelling and molecular docking analysis of selected mutants provided clues for a better accommodation of medium chain-length substrates, and for a modified Zn2+ environment, in agreement with the substrate and temperature profile shifts observed.

Predicting the optimal growth temperatures of prokaryotes using only genome derived features.

Optimal growth temperature is a fundamental characteristic of all living organisms. Knowledge of this temperature is central to the study of a prokaryote, the thermal stability and temperature dependent activity of its genes, and the bioprospecting of its genome for thermally adapted proteins. While high throughput sequencing methods have dramatically increased the availability of genomic information, the growth temperatures of the source organisms are often unknown. This limits the study and technological application of these species and their genomes. Here, we present a novel method for the prediction of growth temperatures of prokaryotes using only genomic sequences. By applying the reverse ecology principle that an organism's genome includes identifiable adaptations to its native environment, we can predict a species' optimal growth temperature with an accuracy of 5.17°C root-mean-square error and a coefficient of determination of 0.835. The accuracy can be further improved for specific taxonomic clades or by excluding psychrophiles. This method provides a valuable tool for the rapid calculation of organism growth temperature when only the genome sequence is known. Source code, genomes analyzed and features calculated are available at: https://github.com/DavidBSauer/OGT_prediction. Supplementary data are available at Bioinformatics online.