scholarly journals Conserved bases for the initial cyclase in gibberellin biosynthesis: from bacteria to plants

2019 ◽  
Vol 476 (18) ◽  
pp. 2607-2621 ◽  
Author(s):  
Cody Lemke ◽  
Kevin C. Potter ◽  
Samuel Schulte ◽  
Reuben J. Peters
Keyword(s):  
Catalytic Mechanism ◽  
Phylogenetic Analyses ◽  
Gibberellin Biosynthesis ◽  
Associated Bacteria ◽  
Functional Conservation ◽  
Microbe Interactions ◽  
Bacteria And Fungi ◽  
Product Outcome ◽  
Insight Into ◽  
Ga Biosynthesis

Abstract All land plants contain at least one class II diterpene cyclase (DTC), which utilize an acid-base catalytic mechanism, for the requisite production of ent-copalyl diphosphate (ent-CPP) in gibberellin A (GA) phytohormone biosynthesis. These ent-CPP synthases (CPSs) are hypothesized to be derived from ancient bacterial origins and, in turn, to have given rise to the frequently observed additional DTCs utilized in more specialized plant metabolism. However, such gene duplication and neo-functionalization has occurred repeatedly, reducing the utility of phylogenetic analyses. Support for evolutionary scenarios can be found in more specific conservation of key enzymatic features. While DTCs generally utilize a DxDD motif as the catalytic acid, the identity of the catalytic base seems to vary depending, at least in part, on product outcome. The CPS from Arabidopsis thaliana has been found to utilize a histidine-asparagine dyad to ligate a water molecule that serves as the catalytic base, with alanine substitution leading to the production of 8β-hydroxy-ent-CPP. Here this dyad and effect of Ala substitution is shown to be specifically conserved in plant CPSs involved in GA biosynthesis, providing insight into plant DTC evolution and assisting functional assignment. Even more strikingly, while GA biosynthesis arose independently in plant-associated bacteria and fungi, the catalytic base dyad also is specifically found in the relevant bacterial, but not fungal, CPSs. This suggests functional conservation of CPSs from bacteria to plants, presumably reflecting an early role for derived diterpenoids in both plant development and plant–microbe interactions, eventually leading to GA, and a speculative evolutionary scenario is presented.

scholarly journals Unraveling a Tangled Skein: Evolutionary Analysis of the Bacterial Gibberellin Biosynthetic Operon

mSphere ◽  
2020 ◽  
Vol 5 (3) ◽  
Author(s):  
Ryan S. Nett ◽  
Huy Nguyen ◽  
Raimund Nagel ◽  
Ariana Marcassa ◽  
Trevor C. Charles ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Genetic Heterogeneity ◽  
Evolutionary History ◽  
Biosynthetic Gene Cluster ◽  
Evolutionary Analysis ◽  
Biosynthetic Gene ◽  
Ancestral Gene ◽  
Associated Bacteria ◽  
Microbe Interactions ◽  
Insight Into

ABSTRACT Gibberellin (GA) phytohormones are ubiquitous regulators of growth and developmental processes in vascular plants. The convergent evolution of GA production by plant-associated bacteria, including both symbiotic nitrogen-fixing rhizobia and phytopathogens, suggests that manipulation of GA signaling is a powerful mechanism for microbes to gain an advantage in these interactions. Although orthologous operons encode GA biosynthetic enzymes in both rhizobia and phytopathogens, notable genetic heterogeneity and scattered operon distribution in these lineages, including loss of the gene for the final biosynthetic step in most rhizobia, suggest varied functions for GA in these distinct plant-microbe interactions. Therefore, deciphering GA operon evolutionary history should provide crucial evidence toward understanding the distinct biological roles for bacterial GA production. To further establish the genetic composition of the GA operon, two operon-associated genes that exhibit limited distribution among rhizobia were biochemically characterized, verifying their roles in GA biosynthesis. This enabled employment of a maximum parsimony ancestral gene block reconstruction algorithm to characterize loss, gain, and horizontal gene transfer (HGT) of GA operon genes within alphaproteobacterial rhizobia, which exhibit the most heterogeneity among the bacteria containing this biosynthetic gene cluster. Collectively, this evolutionary analysis reveals a complex history for HGT of the entire GA operon, as well as the individual genes therein, and ultimately provides a basis for linking genetic content to bacterial GA functions in diverse plant-microbe interactions, including insight into the subtleties of the coevolving molecular interactions between rhizobia and their leguminous host plants. IMPORTANCE While production of phytohormones by plant-associated microbes has long been appreciated, identification of the gibberellin (GA) biosynthetic operon in plant-associated bacteria has revealed surprising genetic heterogeneity. Notably, this heterogeneity seems to be associated with the lifestyle of the microbe; while the GA operon in phytopathogenic bacteria does not seem to vary to any significant degree, thus enabling production of bioactive GA, symbiotic rhizobia exhibit a number of GA operon gene loss and gain events. This suggests that a unique set of selective pressures are exerted on this biosynthetic gene cluster in rhizobia. Through analysis of the evolutionary history of the GA operon in alphaproteobacterial rhizobia, which display substantial diversity in their GA operon structure and gene content, we provide insight into the effect of lifestyle and host interactions on the production of this phytohormone by plant-associated bacteria.

scholarly journals Investigating the Phylogenetic Range of Gibberellin Biosynthesis in Bacteria

2017 ◽  
Vol 30 (4) ◽  
pp. 343-349 ◽  
Author(s):  
Raimund Nagel ◽  
Reuben J. Peters
Keyword(s):  
Fungal Pathogen ◽  
Plant Pathogens ◽  
Bacterial Pathogen ◽  
Xanthomonas Oryzae ◽  
Gibberella Fujikuroi ◽  
Gibberellin Biosynthesis ◽  
Erwinia Tracheiphila ◽  
Associated Bacteria ◽  
Exact Product ◽  
Ga Biosynthesis

Certain plant-associated microbes can produce gibberellin (GA) phytohormones, as first described for the rice fungal pathogen Gibberella fujikuroi and, more recently, for bacteria, including several rhizobia and the rice bacterial pathogen Xanthomonas oryzae pv. oryzicola. The relevant enzymes are encoded by a biosynthetic operon that exhibits both a greater phylogenetic range and scattered distribution among plant-associated bacteria. Here, the phylogenetic distribution of this operon was investigated. To demonstrate conserved functionality, the enzymes encoded by the disparate operon from X. translucens pv. translucens, along with those from the most divergent example, found in Erwinia tracheiphila, were biochemically characterized. In both of these phytopathogens, the operon leads to production of the bioactive GA4. Based on these results, it seems that this operon is widely dedicated to GA biosynthesis. However, there is intriguing variation in the exact product. In particular, although all plant pathogens seem to produce bioactive GA4, rhizobia generally only produce the penultimate hormonal precursor GA9. This is suggested to reflect their distinct interactions with plants, because production of GA4 counteracts the jasmonic-acid-mediated defense response, reflecting the importance of wounds as the entry point for these phytopathogens, whereas such suppression presumably is detrimental in the rhizobial symbiotic relationship.

scholarly journals Response of gut microbiota to feed-borne bacteria depends on fish growth rate: a snapshot survey of farmed juvenile Takifugu obscurus

2020 ◽  
Author(s):  
Xingkun Jin ◽  
Ziwei Chen ◽  
Yan Shi ◽  
Jian-Fang Gui ◽  
Zhe Zhao
Keyword(s):  
Growth Rate ◽  
Gut Microbiota ◽  
Slow Growth ◽  
Ecological Processes ◽  
Associated Bacteria ◽  
Microbe Interactions ◽  
Environmental Bacteria ◽  
Feed Source ◽  
Host Microbe Interactions ◽  
Insight Into

ABSTRACTUnderstanding the ecological processes in controlling the assemblage of gut microbiota becomes an essential prerequisite for a more sustainable aquaculture. Here we used 16S rRNA amplicon sequencing to characterize the hindgut microbiota from cultured obscure puffer Takifugu obscurus. The gut microbiota is featured with lower alpha-diversity, greater beta-dispersion and higher average 16S rRNA copy numbers comparing to water and sediment, but far less so to feed. SourceTracker predicted a notable source signature from feed in gut microbiota. Furthermore, effect of varying degrees of feed-associated bacteria on compositional, functional and phylogenetic diversity of gut microbiota were revealed. Coincidently, considerable increase of species richness and feed source proportions both were observed in slow growth fugu, implying a reduced stability in gut microbiota upon bacterial disturbance from feed. Moreover, quantitative ecological analytic framework was applied and the ecological processes underlying such community shift were determined. In the context of lower degree of feed disturbance, homogeneous selection and dispersal limitation largely contribute to the community stability and partial variations among hosts. Whilst with the degree of feed disturbance increased, variable selection leads to an augmented interaction within gut microbiota, entailing community unstability and shift. Altogether, our findings illustrated a clear diversity-function relationships in fugu gut microbiota, and it has implicated in a strong correlation between feed-borne bacteria and host growth rate. These results provide a new insight into aquaculture of fugu and other economically important fishes, as well as a better understanding of host-microbe interactions in the vertebrate gastrointestinal tract.IMPORTANCEEnvironmental bacteria has a great impact on fish gut microbiota, yet little is known as to where fish acquire their gut symbionts, and how gut microbiota response to environmental bacteria. Through the integrative analysis by community profiling and source tracking, we show that feed-associated bacteria can impose a strong disturbance upon fugu gut microbiota. As a result, marked alterations in the composition and function of gut microbiota in slow growth fugu were observed, which is potentially correlated with the host physiological condition such as gastric evacuation rate. Our findings emphasized the intricate linkage between feed and gut microbiota, and highlighted the importance of resolving the feed source signal before the conclusion of comparative analysis of microbiota can be drawn. Our results provide a deeper insight into aquaculture of fugu and other economically important fishes, and have further implications for an improved understanding of host-microbe interactions in the vertebrate gastrointestinal tract.

scholarly journals Identification and Diversity of Bacterial Communities Associated with the Venom Glands of the Fire Ant, Solenopsis invicta Buren (Hymenoptera: Formicidae)

2020 ◽  
Author(s):  
Fan Yang ◽  
Jinyong Yu ◽  
Siqi Chen ◽  
Dongdong Ning ◽  
Babar Hassan ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Solenopsis Invicta ◽  
Fire Ant ◽  
Diversity Analysis ◽  
Associated Bacteria ◽  
Solenopsis Invicta Buren ◽  
Venom Glands ◽  
Microbe Interactions ◽  
Insight Into

Abstract Background Ant-microbe interactions that naturally occur in the venom microenvironment remain mostly unknown. To best of our knowledge, no research exists that shows the identity and diversity of bacterial communities in the fires ants, and what adaptive advantages that venom-associated microbes might offer to their hosts or that hosts might provide to venom-associated bacteria. This study assessed the diversity and identity of bacteria associated with the venom glands of Solenopsis invicta and compared this community with the bacterial communities of two other stinging ants, Solenopsis geminata and Diacamma rugosum. Results The major phylum associated with the venom glands of S. invicta (workers, alates, and queens) and S. geminata (workers) was Proteobacteria, while Firmicutes were abundant in the venom glands of D. rugosum (workers). Tenericutes were also more abundant in the venom glands of S. invicta queens than in those of workers and alates. The relative abundance of Spiroplasma in S. geminata was significantly higher than those in D. rugosum and S. invicta. A microbial diversity analysis of venom glands of worker ants of Solenopsis species showed that the relative abundances of Bacillus and Lactococcus were higher in Guangxi S. invicta workers than in workers collected from Guangzhou. However, the abundance of Lactococcus in workers of D. rugosum was higher than those in workers of S. geminata from Guangxi and S. invicta collected from Guangzhou. Conclusions This study provides the first insight into the microbiota in the venom glands of S. invicta, S. geminata, and D. rugosum, which might contribute to a more comprehensive view of the role of bacteria in the synthesis or degradation of active venom components in the host. We hypothesized that the differences in bacterial communities of three ant species could be due to the local adaptation of insects along with the coevolution of bacteria and hosts.

Copper–oxygen Dynamics in Tyrosinase

2019 ◽  
Author(s):  
Nobutaka Fujieda ◽  
Sachiko Yanagisawa ◽  
Minoru Kubo ◽  
Genji Kurisu ◽  
Shinobu Itoh
Keyword(s):  
Catalytic Mechanism ◽  
Substrate Binding ◽  
Active Form ◽  
Copper Ion ◽  
Atomic Resolution ◽  
Oxygen Species ◽  
X Ray ◽  
Oxygen Dynamics ◽  
Insight Into ◽  
Copper Centre

To unveil the activation of dioxygen on the copper centre (Cu<sub>2</sub>O<sub>2</sub>core) of tyrosinase, we performed X-ray crystallograpy with active-form tyrosinase at near atomic resolution. This study provided a novel insight into the catalytic mechanism of the tyrosinase, including the rearrangement of copper-oxygen species as well as the intramolecular migration of copper ion induced by substrate-binding.<br>

scholarly journals Crystallographic insight into the catalytic mechanism of subunit A of the A-ATP synthase and the P-loop switch in evolution

2010 ◽  
Vol 1797 ◽  
pp. 32-33
Author(s):  
Anil Kumar ◽  
Malathy Sony Subramanian Manimekalai ◽  
Asha Manikkoth Balakrishna ◽  
Gerhard Grüber
Keyword(s):  
Atp Synthase ◽  
Catalytic Mechanism ◽  
Subunit A ◽  
Insight Into

Multifaceted Impacts of Bacteriophages in the Plant Microbiome

2018 ◽  
Vol 56 (1) ◽  
pp. 361-380 ◽  
Author(s):  
Britt Koskella ◽  
Tiffany B. Taylor
Keyword(s):  
Host Plant ◽  
Future Study ◽  
Plant Pathogens ◽  
Ecological Interactions ◽  
Selection Pressures ◽  
Bacterial Populations ◽  
Associated Bacteria ◽  
Open Questions ◽  
Microbe Interactions ◽  
Plant Microbiome

Plant-associated bacteria face multiple selection pressures within their environments and have evolved countless adaptations that both depend on and shape bacterial phenotype and their interaction with plant hosts. Explaining bacterial adaptation and evolution therefore requires considering each of these forces independently as well as their interactions. In this review, we examine how bacteriophage viruses (phages) can alter the ecology and evolution of plant-associated bacterial populations and communities. This includes influencing a bacterial population's response to both abiotic and biotic selection pressures and altering ecological interactions within the microbiome and between the bacteria and host plant. We outline specific ways in which phages can alter bacterial phenotype and discuss when and how this might impact plant-microbe interactions, including for plant pathogens. Finally, we highlight key open questions in phage-bacteria-plant research and offer suggestions for future study.

scholarly journals Extensive Horizontal Gene Transfer in Cheese-Associated Bacteria

2016 ◽  
Author(s):  
Kevin S. Bonham ◽  
Benjamin E. Wolfe ◽  
Rachel J. Dutton
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Molecular Mechanisms ◽  
Protein Coding ◽  
Associated Bacteria ◽  
The Us ◽  
Selective Forces ◽  
Genomic Regions ◽  
Microbiome Assembly ◽  
Insight Into

AbstractAcquisition of genes through horizontal gene transfer (HGT) allows microbes to rapidly gain new capabilities and adapt to new or changing environments. Identifying widespread HGT regions within multispecies microbiomes can pinpoint the molecular mechanisms that play key roles in microbiome assembly. We sought to identify horizontally transferred genes within a model microbiome, the cheese rind. Comparing 31 newly-sequenced and 134 previously sequenced bacterial isolates from cheese rinds, we identified over 200 putative horizontally transferred genomic regions containing 4,733 protein coding genes. The largest of these regions are enriched for genes involved in siderophore acquisition, and are widely distributed in cheese rinds in both Europe and the US. These results suggest that horizontal gene transfer (HGT) is prevalent in cheese rind microbiomes, and the identification of genes that are frequently transferred in a particular environment may provide insight into the selective forces shaping microbial communities.

scholarly journals Functional conservation and divergence of five AP1/FUL-like genes in Marigold (Tagetes erecta)

2020 ◽  
Author(s):  
Chunling Zhang ◽  
Yalin Sun ◽  
Ludan Wei ◽  
Wenjing Wang ◽  
Hang Li ◽  
...  
Keyword(s):  
Profile Analysis ◽  
Floral Organ ◽  
Tagetes Erecta ◽  
Functional Conservation ◽  
Floral Buds ◽  
Expression Profile Analysis ◽  
Petal Identity ◽  
Organ Identity ◽  
Insight Into

Abstract Background: Members of AP1/FUL subfamily genes play an essential role in the regulation of floral meristem transition, floral organ identity, and fruit ripping. At present, there have been insufficient studies to explain the function of the AP1/FUL-like subfamily genes in Asteraceae. Results: Here, we cloned two euAP1 clade genes TeAP1-1 and TeAP1-2, and three euFUL clade genes TeFUL1, TeFUL2, and TeFUL3 from marigold (Tagetes erecta). Expression profile analysis demonstrated that TeAP1-1 and TeAP1-2 were mainly expressed in receptacles, sepals, petals, and ovules. TeFUL1 and TeFUL3 were expressed in floral buds, stems and leaves as well as in productive tissues, while TeFUL2 was mainly expressed in floral buds and vegetative tissues. Transgenic Arabidopsis lines showed that overexpression TeAP1-2 or TeFUL2 resulted in early flowering, implying that these two genes might regulate the floral transition. Yeast two-hybrid analysis indicated that TeAP1/FUL proteins only interacted with TeSEP proteins to form heterodimers, and that TeFUL2 could also form a homodimer.Conclusion: In general, TeAP1-1 and TeAP1-2 might play a conserved role in regulating sepal and petal identity, just like the role of MADS-box class A genes, while TeFUL genes might display divergent functions. This study provides an insight into molecular mechanism of AP1/FUL-like genes in Asteraceae species.

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