Title: Regulation of tricarboxylate transport and metabolism in Acinetobacter baylyi ADP1
ABSTRACT Despite the significant presence of plant-derived tricarboxylic acids in some environments, few studies detail the bacterial metabolism oftrans-aconitic acid (Taa) and tricarballylic acid (Tcb). In a soil bacterium,Acinetobacter baylyiADP1, we discovered interrelated pathways for the consumption of Taa and Tcb. An intricate regulatory scheme tightly controls the transport and catabolism of both compounds and may reflect that they can be toxic inhibitors of the tricarboxylic acid cycle. The genes encoding two similar LysR-type transcriptional regulators, TcuR and TclR, were clustered on the chromosome withtcuAandtcuB, genes required for Tcb consumption. The genetic organization differed from that inSalmonella entericaserovar Typhimurium, in whichtcuAandtcuBform an operon with a transporter gene,tcuC. InA. baylyi,tcuCwas not cotranscribed withtcuAB. Rather,tcuCwas cotranscribed with a gene, designatedpacI, encoding an isomerase needed for Taa consumption. TcuC appears to transport Tcb andcis-aconitic acid (Caa), the presumed product of PacI-mediated periplasmic isomerization of Taa. Two operons,tcuC-pacIandtcuAB, were transcriptionally controlled by both TcuR and TclR, which have overlapping functions. We investigated the roles of the two regulators in activating transcription of both operons in response to multiple effector compounds, including Taa, Tcb, and Caa.IMPORTANCEIngestion of Taa and Tcb by grazing livestock can cause a serious metabolic disorder called grass tetany. The disorder, which results from Tcb absorption by ruminants, focuses attention on the metabolism of tricarboxylic acids. Additional interest stems from efforts to produce tricarboxylic acids as commodity chemicals. Improved understanding of bacterial enzymes and pathways for tricarboxylic acid metabolism may contribute to new biomanufacturing strategies. more »« less
Tubergen, Philip J.; Medlock, Greg; Moore, Anni; Zhang, Xiaomu; Papin, Jason A.; Danna, Cristian H.
(, PLOS Computational Biology)
Wallqvist, Anders
(Ed.)
Bacterial pathogens adapt their metabolism to the plant environment to successfully colonize their hosts. In our efforts to uncover the metabolic pathways that contribute to the colonization ofArabidopsis thalianaleaves byPseudomonas syringaepvtomatoDC3000 (PstDC3000), we created iPst19, an ensemble of 100 genome-scale network reconstructions ofPstDC3000 metabolism. We developed a novel approach for gene essentiality screens, leveraging the predictive power of iPst19 to identify core and ancillary condition-specific essential genes. Constraining the metabolic flux of iPst19 withPstDC3000 gene expression data obtained from naïve-infected or pre-immunized-infected plants, revealed changes in bacterial metabolism imposed by plant immunity. Machine learning analysis revealed that among other amino acids, branched-chain amino acids (BCAAs) metabolism significantly contributed to the overall metabolic status of each gene-expression-contextualized iPst19 simulation. These predictions were tested and confirmed experimentally.PstDC3000 growth and gene expression analysis showed that BCAAs suppress virulence gene expressionin vitrowithout affecting bacterial growth.In planta, however, an excess of BCAAs suppress the expression of virulence genes at the early stages of infection and significantly impair the colonization of Arabidopsis leaves. Our findings suggesting that BCAAs catabolism is necessary to express virulence and colonize the host. Overall, this study provides valuable insights into how plant immunity impactsPstDC3000 metabolism, and how bacterial metabolism impacts the expression of virulence.
Wilson, Nathan; Smith-Moore, Caroline; Xu, Yuan; Edwards, Brianne; La_Hovary, Christophe; Li, Kai; Aslett, Denise; Ji, Mikyoung; Lin, Xuli; Vintila, Simina; et al
(, Frontiers in Plant Science)
IntroductionPlants employ the Calvin-Benson cycle (CBC) to fix atmospheric CO2for the production of biomass. The flux of carbon through the CBC is limited by the activity and selectivity of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (RuBisCO). Alternative CO2fixation pathways that do not use RuBisCO to fix CO2have evolved in some anaerobic, autotrophic microorganisms. MethodsRather than modifying existing routes of carbon metabolism in plants, we have developed a synthetic carbon fixation cycle that does not exist in nature but is inspired by metabolisms of bacterial autotrophs. In this work, we build and characterize a condensed, reverse tricarboxylic acid (crTCA) cyclein vitroandin planta. ResultsWe demonstrate that a simple, synthetic cycle can be used to fix carbon in vitro under aerobic and mesophilic conditions and that these enzymes retain activity whenexpressed transientlyin planta. We then evaluate stable transgenic lines ofCamelina sativathat have both phenotypic and physiologic changes. TransgenicC. sativaare shorter than controls with increased rates of photosynthetic CO2assimilation and changes in photorespiratory metabolism. DiscussionThis first iteration of a build-test-learn phase of the crTCA cycle provides promising evidence that this pathway can be used to increase photosynthetic capacity in plants.
Xiang, Xiaoqin; Deng, Qianxia; Zheng, Yi; He, Yi; Ji, Dongpu; Vejlupkova, Zuzana; Fowler, John E; Zhou, Lian
(, BMC Plant Biology)
Abstract BackgroundThe La-related proteins (LARPs) are a superfamily of RNA-binding proteins associated with regulation of gene expression. Evidence points to an important role for post-transcriptional control of gene expression in germinating pollen tubes, which could be aided by RNA-binding proteins. ResultsIn this study, a genome-wide investigation of the LARP proteins in eight plant species was performed. The LARP proteins were classified into three families based on a phylogenetic analysis. The gene structure, conserved motifs,cis-acting elements in the promoter, and gene expression profiles were investigated to provide a comprehensive overview of the evolutionary history and potential functions ofZmLARPgenes in maize. Moreover,ZmLARP6c1was specifically expressed in pollen and ZmLARP6c1 was localized to the nucleus and cytoplasm in maize protoplasts. Overexpression ofZmLARP6c1enhanced the percentage pollen germination compared with that of wild-type pollen. In addition, transcriptome profiling analysis revealed that differentially expressed genes includedPABPhomologous genes and genes involved in jasmonic acid and abscisic acid biosynthesis, metabolism, signaling pathways and response in aZmlarp6c1::Dsmutant andZmLARP6c1-overexpression line compared with the corresponding wild type. ConclusionsThe findings provide a basis for further evolutionary and functional analyses, and provide insight into the critical regulatory function ofZmLARP6c1in maize pollen germination.
Nwokocha, George C; Ghosh, Arpita; Grove, Anne
(, Journal of Bacteriology)
O'Toole, George
(Ed.)
ABSTRACT Bacterial plant pathogens adjust their gene expression programs in response to environmental signals and host-derived compounds. This ensures that virulence genes or genes encoding proteins, which promote bacterial fitness in a host environment, are expressed only when needed. Such regulation is in the purview of transcription factors, many of which belong to the ubiquitous multiple antibiotic resistance regulator (MarR) protein family. PecS proteins constitute a subset of this large protein family. PecS has likely been distributed by horizontal gene transfer, along with the divergently encoded efflux pump PecM, suggesting its integration into existing gene regulatory networks. Here, we discuss the roles of PecS in the regulation of genes associated with virulence and fitness of bacterial plant pathogens. A comparison of phenotypes and differential gene expression associated with the disruption of pecS shows that functional consequences of PecS integration into existing transcriptional networks are highly variable, resulting in distinct PecS regulons. Although PecS universally binds to the pecS-pecM intergenic region to repress the expression of both genes, binding modes differ. A particularly relaxed sequence preference appears to apply for Dickeya dadantii PecS, perhaps to optimize its integration as a global regulator and regulate genes ancestral to the acquisition of pecS-pecM. Even inducing ligands for PecS are not universally conserved. It appears that PecS function has been optimized to match the unique regulatory needs of individual bacterial species and that its roles must be appreciated in the context of the regulatory networks into which it was recruited.
Abstract BackgroundMorphologic sex differences between males and females typically emerge after the primordial germ cell migration and gonad formation, although sex is determined at fertilization based on chromosome composition. A key debated sexual difference is the embryonic developmental rate, within vitroproduced male embryos often developing faster. However, the molecular mechanisms driving early embryonic sex differences remain unclear. ResultsTo investigate the transcriptional sex difference during early development,in vitroproduced bovine blastocysts were collected and sexed by PCR. A significant male-biased development was observed in expanded blastocysts. Ultra-low input RNA-seq analysis identified 837 DEGs, with 231 upregulated and 606 downregulated in males. Functional enrichment analysis revealed male-biased DEGs were associated with metabolic regulation, whereas female-biased DEGs were related to female gonad development, sex differentiation, inflammatory pathways, and TGF-beta signaling. Comparing X chromosome and autosome expression ratio, we found that female-biased DEGs contributed to the higher X-linked gene dosage, a phenomenon not observed in male embryos. Moreover, we identified the sex-biased transcription factors and RNA-bind proteins, including pluripotent factors such asSOX21andPRDM14, and splicing factorsFMR1andHNRNPH2. Additionally, we revealed 1,555 significantly sex-biased differential alternative splicing (AS), predominantly skipped exons, mapped to 906 genes, with 59 overlapping with DEGs enriched in metabolic and autophagy pathways. By incorporating novel isoforms from long reads sequencing, we identified 1,151 sex-biased differentially expressed isoforms (DEIs) associated with 1,017 genes. Functional analysis showed that female-biased DEIs were involved in the negative regulation of transcriptional activity, while male-biased DEIs were related to energy metabolism. Furthermore, we identified sex-biased differential exon usage inDENND1B, DIS3L2, DOCK11, IL1RAPL2,andZRSR2Y,indicating their sex-specific regulation in early embryo development. ConclusionThis study provided a comprehensive analysis of transcriptome differences between male and female bovine blastocysts, integrating sex-biased gene expression, alternative splicing, and isoform dynamics. Our findings indicate that enriched metabolism processes in male embryos may contribute to the faster developmental pace, providing insights into sex-specific regulatory mechanisms during early embryogenesis. Plain English summaryMale and female early embryos develop at different speeds, with male embryos often developing faster than female embryos. However, the reasons behind these early differences remain unclear. In this study, we examined gene activity in bovine embryos to uncover the biological factors regulating these early sex differences. We collected in vitro-produced bovine blastocysts, examined their sex, and confirmed that male embryos develop faster. By analyzing global gene activity, including alternative splicing, which allows one gene to code for multiple RNA isoforms and proteins, we found distinct gene expression profiles between male and female embryos. Male embryos showed higher activity in genes related to metabolism and cellular functions, while female embryos had increased activity in genes associated with female-specific gonad development and gene expression regulation. We also examined differences in how genes on the X chromosome were expressed. Female embryos had higher X-linked gene expression, which may contribute to sex-specific developmental regulation. Additionally, we identified sex-specific transcription factors and RNA-binding proteins that regulate early embryo development, some of which are known to control pluripotency and gene splicing. Overall, our study provides new insights into how gene activity shapes early sex differences, suggesting that enhanced metabolism in male embryos may be a key driver of their faster developmental rate. HighlightsMale embryos develop faster due to increased gene expression in metabolism pathwaysFemale embryos exhibit higher X-linked gene expression, suggesting X-dosage compensation plays a role in early developmentSex-biased alternative splicing events contribute to embryonic metabolism, autophagy, and transcriptional regulation in embryosSex-biased isoform diversity contributes to distinct developmental regulation in male and female embryosKey pluripotency factors (SOX21, PRDM14) and splicing regulators (FMR1, HNRNPH2) drive sex-specific gene expression
Baugh, Alyssa C, Defalco, Justin B, Duscent-Maitland, Chantel V, Tumen-Velasquez, Melissa P, Laniohan, Nicole S, Figatner, Kayla, Hoover, Timothy R, Karls, Anna C, Elliott, Kathryn T, and Neidle, Ellen L. Regulation of tricarboxylate transport and metabolism in Acinetobacter baylyi ADP1. Retrieved from https://par.nsf.gov/biblio/10536410. Applied and Environmental Microbiology 90.2 Web. doi:10.1128/aem.02111-23.
Baugh, Alyssa C, Defalco, Justin B, Duscent-Maitland, Chantel V, Tumen-Velasquez, Melissa P, Laniohan, Nicole S, Figatner, Kayla, Hoover, Timothy R, Karls, Anna C, Elliott, Kathryn T, and Neidle, Ellen L.
"Regulation of tricarboxylate transport and metabolism in Acinetobacter baylyi ADP1". Applied and Environmental Microbiology 90 (2). Country unknown/Code not available: ASM. https://doi.org/10.1128/aem.02111-23.https://par.nsf.gov/biblio/10536410.
@article{osti_10536410,
place = {Country unknown/Code not available},
title = {Regulation of tricarboxylate transport and metabolism in Acinetobacter baylyi ADP1},
url = {https://par.nsf.gov/biblio/10536410},
DOI = {10.1128/aem.02111-23},
abstractNote = {ABSTRACT Despite the significant presence of plant-derived tricarboxylic acids in some environments, few studies detail the bacterial metabolism oftrans-aconitic acid (Taa) and tricarballylic acid (Tcb). In a soil bacterium,Acinetobacter baylyiADP1, we discovered interrelated pathways for the consumption of Taa and Tcb. An intricate regulatory scheme tightly controls the transport and catabolism of both compounds and may reflect that they can be toxic inhibitors of the tricarboxylic acid cycle. The genes encoding two similar LysR-type transcriptional regulators, TcuR and TclR, were clustered on the chromosome withtcuAandtcuB, genes required for Tcb consumption. The genetic organization differed from that inSalmonella entericaserovar Typhimurium, in whichtcuAandtcuBform an operon with a transporter gene,tcuC. InA. baylyi,tcuCwas not cotranscribed withtcuAB. Rather,tcuCwas cotranscribed with a gene, designatedpacI, encoding an isomerase needed for Taa consumption. TcuC appears to transport Tcb andcis-aconitic acid (Caa), the presumed product of PacI-mediated periplasmic isomerization of Taa. Two operons,tcuC-pacIandtcuAB, were transcriptionally controlled by both TcuR and TclR, which have overlapping functions. We investigated the roles of the two regulators in activating transcription of both operons in response to multiple effector compounds, including Taa, Tcb, and Caa.IMPORTANCEIngestion of Taa and Tcb by grazing livestock can cause a serious metabolic disorder called grass tetany. The disorder, which results from Tcb absorption by ruminants, focuses attention on the metabolism of tricarboxylic acids. Additional interest stems from efforts to produce tricarboxylic acids as commodity chemicals. Improved understanding of bacterial enzymes and pathways for tricarboxylic acid metabolism may contribute to new biomanufacturing strategies.},
journal = {Applied and Environmental Microbiology},
volume = {90},
number = {2},
publisher = {ASM},
author = {Baugh, Alyssa C and Defalco, Justin B and Duscent-Maitland, Chantel V and Tumen-Velasquez, Melissa P and Laniohan, Nicole S and Figatner, Kayla and Hoover, Timothy R and Karls, Anna C and Elliott, Kathryn T and Neidle, Ellen L},
editor = {Cann, Isaac}
}
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