1
|
Jeong S, Singh H, Jung JH, Jung KW, Ryu S, Lim S. Comparative genomics of Deinococcus radiodurans: unveiling genetic discrepancies between ATCC 13939K and BAA-816 strains. Front Microbiol 2024; 15:1410024. [PMID: 38962131 PMCID: PMC11219805 DOI: 10.3389/fmicb.2024.1410024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Accepted: 06/04/2024] [Indexed: 07/05/2024] Open
Abstract
The Deinococcus genus is renowned for its remarkable resilience against environmental stresses, including ionizing radiation, desiccation, and oxidative damage. This resilience is attributed to its sophisticated DNA repair mechanisms and robust defense systems, enabling it to recover from extensive damage and thrive under extreme conditions. Central to Deinococcus research, the D. radiodurans strains ATCC BAA-816 and ATCC 13939 facilitate extensive studies into this remarkably resilient genus. This study focused on delineating genetic discrepancies between these strains by sequencing our laboratory's ATCC 13939 specimen (ATCC 13939K) and juxtaposing it with ATCC BAA-816. We uncovered 436 DNA sequence differences within ATCC 13939K, including 100 single nucleotide variations, 278 insertions, and 58 deletions, which could induce frameshifts altering protein-coding genes. Gene annotation revisions accounting for gene fusions and the reconciliation of gene lengths uncovered novel protein-coding genes and refined the functional categorizations of established ones. Additionally, the analysis pointed out genome structural variations due to insertion sequence (IS) elements, underscoring the D. radiodurans genome's plasticity. Notably, ATCC 13939K exhibited a loss of six ISDra2 elements relative to BAA-816, restoring genes fragmented by ISDra2, such as those encoding for α/β hydrolase and serine protease, and revealing new open reading frames, including genes imperative for acetoin decomposition. This comparative genomic study offers vital insights into the metabolic capabilities and resilience strategies of D. radiodurans.
Collapse
Affiliation(s)
- Soyoung Jeong
- Radiation Biotechnology Division, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
- Department of Food and Animal Biotechnology, Seoul National University, Seoul, Republic of Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Harinder Singh
- Department of Biological Sciences, Sunandan Divatia School of Science, NMIMS Deemed to be University, Mumbai, India
| | - Jong-Hyun Jung
- Radiation Biotechnology Division, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Kwang-Woo Jung
- Radiation Biotechnology Division, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Sangryeol Ryu
- Department of Food and Animal Biotechnology, Seoul National University, Seoul, Republic of Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Sangyong Lim
- Radiation Biotechnology Division, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
- Department of Radiation Science, University of Science and Technology, Daejeon, Republic of Korea
| |
Collapse
|
2
|
Epiktetov DO, Sviridov AV, Tarlachkov SV, Shushkova TV, Toropygin IY, Leontievsky AA. Glyphosate-Induced Phosphonatase Operons in Soil Bacteria of the Genus Achromobacter. Int J Mol Sci 2024; 25:6409. [PMID: 38928116 PMCID: PMC11203657 DOI: 10.3390/ijms25126409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/24/2024] [Accepted: 05/28/2024] [Indexed: 06/28/2024] Open
Abstract
Achromobacter insolitus and Achromobacter aegrifaciens, bacterial degraders of the herbicide glyphosate, were found to induce phosphonatase (phosphonoacetaldehyde hydrolase, EC 3.11.1.1) when grown on minimal media with glyphosate as the sole source of phosphorus. The phosphonatases of the strains were purified to an electrophoretically homogeneous state and characterized. The enzymes differed in their kinetic characteristics and some other parameters from the previously described phosphonatases. The phosphonatase of A. insolitus was first revealed to separate into two stable forms, which had similar kinetic characteristics but interacted differently with affinity and ion-exchange resins. The genomes of the investigated bacteria were sequenced. The phosphonatase genes were identified, and their context was determined: the bacteria were shown to have gene clusters, which, besides the phosphonatase operon, included genes for LysR-type transcription activator (substrate sensor) and putative iron-containing oxygenase PhnHD homologous to monooxygenases PhnY and TmpB of marine organophosphonate degraders. Genes of 2-aminoethylphosphonate aminotransferase (PhnW, EC 2.6.1.37) were absent in the achromobacterial phosphonatase operons; instead, we revealed the presence of genes encoding the putative flavin oxidase HpnW. In silico simulation showed 1-hydroxy-2-aminoethylphosphonate to be the most likely substrate of the new monooxygenase, and a number of glycine derivatives structurally similar to glyphosate to be substrates of flavin oxidase.
Collapse
Affiliation(s)
- Dmitry O. Epiktetov
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Russian Academy of Sciences, 5 Prosp. Nauki, 142290 Pushchino, Russia; (D.O.E.); (S.V.T.); (T.V.S.); (A.A.L.)
| | - Alexey V. Sviridov
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Russian Academy of Sciences, 5 Prosp. Nauki, 142290 Pushchino, Russia; (D.O.E.); (S.V.T.); (T.V.S.); (A.A.L.)
| | - Sergey V. Tarlachkov
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Russian Academy of Sciences, 5 Prosp. Nauki, 142290 Pushchino, Russia; (D.O.E.); (S.V.T.); (T.V.S.); (A.A.L.)
- Branch of Shemyakin—Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Puschino, 142290 Moscow, Russia
| | - Tatyana V. Shushkova
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Russian Academy of Sciences, 5 Prosp. Nauki, 142290 Pushchino, Russia; (D.O.E.); (S.V.T.); (T.V.S.); (A.A.L.)
| | - Ilya Yu. Toropygin
- V.N. Orekhovich Research Institute of Biomedical Chemistry, Bld. 8, 10 Pogodinskaya Str., 119121 Moscow, Russia;
| | - Alexey A. Leontievsky
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Russian Academy of Sciences, 5 Prosp. Nauki, 142290 Pushchino, Russia; (D.O.E.); (S.V.T.); (T.V.S.); (A.A.L.)
| |
Collapse
|
3
|
Supty MSA, Jahan K, Lee JS, Choi KH. Epiphytic Bacterial Community Analysis of Ulva prolifera in Garorim and Muan Bays, Republic of Korea. Microorganisms 2024; 12:1142. [PMID: 38930524 PMCID: PMC11205692 DOI: 10.3390/microorganisms12061142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/16/2024] [Accepted: 06/02/2024] [Indexed: 06/28/2024] Open
Abstract
The bacterial communities related to seaweed can vary considerably across different locations, and these variations influence the seaweed's nutrition, growth, and development. To study this further, we evaluated the bacteria found on the green marine seaweed Ulva prolifera from Garorim Bay and Muan Bay, two key locations on Republic of Korea's west coast. Our analysis found notable differences in the bacterial communities between the two locations. Garorim Bay hosted a more diverse bacterial population, with the highest number of ASVs (871) compared to Muan Bay's 156 ASVs. In Muan Bay, more than 50% of the bacterial community was dominated by Pseudomonadota. On the other hand, Garorim Bay had a more balanced distribution between Bacteroidota and Pseudomonadota (37% and 35.5%, respectively). Additionally, Cyanobacteria, particularly Cyanothece aeruginosa, were found in significant numbers in Garorim Bay, making up 8% of the community. Mineral analysis indicated that Garorim Bay had higher levels of S, Na, Mg, Ca, and Fe. Function-wise, both locations exhibited bacterial enrichment in amino acid production, nucleosides, and nucleotide pathways. In conclusion, this study broadens our understanding of the bacterial communities associated with Ulva prolifera in Korean waters and provides a foundation for future research on the relationships between U. prolifera and its bacteria.
Collapse
Affiliation(s)
| | | | | | - Keun-Hyung Choi
- Department of Earth, Environmental and Space Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| |
Collapse
|
4
|
Shivangi, Khan Y, Ekka MK, Meena LS. Structural and functional characterization of mycobacterial PhoH2 and identification of potential inhibitor of its enzymatic activity. Braz J Microbiol 2024; 55:1033-1051. [PMID: 38386260 PMCID: PMC11153397 DOI: 10.1007/s42770-024-01267-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 01/30/2024] [Indexed: 02/23/2024] Open
Abstract
Mycobacterium tuberculosis is composed of a cumbersome signaling and protein network which partakes in bacterial survival and augments its pathogenesis. Mycobacterial PhoH2 (Mt-PhoH2) is a signaling element and a predictive phosphate starvation protein that works in an ATP-dependent manner. Here, we elaborated the characterization of Mt-PhoH2 through biophysical, biochemical, and computational methods. In addition to its intrinsic ATPase activity, the biochemical experiments revealed its GTPase activity and both activities are metal ion dependent. Magnesium, manganese, copper, iron, nickel, zinc, cesium, calcium, and lithium were examined for their effect on activity, and the optimum activity was found with 10 mM of Mg2+ ions. The kinetic parameters of 3 µM Mt-PhoH2 were observed as Km 4.873 ± 0.44 µM, Vmax 12.3817 ± 0.084 µM/min/mg, Kcat 0.0075 ± 0.00005 s-1, and Kcat/Km 0.0015 ± 0.000001 µM-1 s-1 with GTP. In the case of GTP as a substrate, a 20% decrease in enzymatic activity and a 50% increase in binding affinity of Mt-PhoH2 were observed. The substrates ADP and GDP inhibit the ATPase and GTPase activity of Mt-PhoH2. CD spectroscopy showed the dominance of alpha helix in the secondary structure of Mt-PhoH2, and this structural pattern was altered upon addition of ATP and GTP. In silico inhibitor screening revealed ML141 and NAV_2729 as two potential inhibitors of the catalytic activity of Mt-PhoH2. Mt-PhoH2 is essential for mycobacterial growth as its knockdown strain showed a decreased growth effect. Overall, the present article emphasizes the factors essential for the proper functioning of Mt-PhoH2 which is a participant in the toxin-antitoxin machinery and may also play an important role in phosphate starvation.
Collapse
Affiliation(s)
- Shivangi
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad, Uttar Pradesh, 201 002, India
| | - Yasmeen Khan
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad, Uttar Pradesh, 201 002, India
| | - Mary Krishna Ekka
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad, Uttar Pradesh, 201 002, India
| | - Laxman S Meena
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007, India.
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad, Uttar Pradesh, 201 002, India.
- CSIR-Central Drug Research Institute, Lucknow, 226031, India.
- CSIR-Institute of Genomics and Integrative Biology, Academy of Scientific & Innovative Research (AcSIR), Mall Road, Delhi, 110007, India.
| |
Collapse
|
5
|
Pettersen JS, Nielsen FD, Andreassen PR, Møller-Jensen J, Jørgensen M. A comprehensive analysis of pneumococcal two-component system regulatory networks. NAR Genom Bioinform 2024; 6:lqae039. [PMID: 38650915 PMCID: PMC11034029 DOI: 10.1093/nargab/lqae039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 04/04/2024] [Accepted: 04/12/2024] [Indexed: 04/25/2024] Open
Abstract
Two-component systems are key signal-transduction systems that enable bacteria to respond to a wide variety of environmental stimuli. The human pathogen, Streptococcus pneumoniae (pneumococcus) encodes 13 two-component systems and a single orphan response regulator, most of which are significant for pneumococcal pathogenicity. Mapping the regulatory networks governed by these systems is key to understand pneumococcal host adaptation. Here we employ a novel bioinformatic approach to predict the regulons of each two-component system based on publicly available whole-genome sequencing data. By employing pangenome-wide association studies (panGWAS) to predict genotype-genotype associations for each two-component system, we predicted regulon genes of 11 of the pneumococcal two-component systems. Through validation via next-generation RNA-sequencing on response regulator overexpression mutants, several top candidate genes predicted by the panGWAS analysis were confirmed as regulon genes. The present study presents novel details on multiple pneumococcal two-component systems, including an expansion of regulons, identification of candidate response regulator binding motifs, and identification of candidate response regulator-regulated small non-coding RNAs. We also demonstrate a use for panGWAS as a complementary tool in target gene identification via identification of genotype-to-genotype links. Expanding our knowledge on two-component systems in pathogens is crucial to understanding how these bacteria sense and respond to their host environment, which could prove useful in future drug development.
Collapse
Affiliation(s)
- Jens Sivkær Pettersen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Flemming Damgaard Nielsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
| | | | - Jakob Møller-Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Mikkel Girke Jørgensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| |
Collapse
|
6
|
Qiu GW, Zheng WC, Yang HM, Wang YY, Qi X, Huang D, Dai GZ, Shi H, Price NM, Qiu BS. Phosphorus deficiency alleviates iron limitation in Synechocystis cyanobacteria through direct PhoB-mediated gene regulation. Nat Commun 2024; 15:4426. [PMID: 38789507 PMCID: PMC11126600 DOI: 10.1038/s41467-024-48847-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 05/14/2024] [Indexed: 05/26/2024] Open
Abstract
Iron and phosphorus are essential nutrients that exist at low concentrations in surface waters and may be co-limiting resources for phytoplankton growth. Here, we show that phosphorus deficiency increases the growth of iron-limited cyanobacteria (Synechocystis sp. PCC 6803) through a PhoB-mediated regulatory network. We find that PhoB, in addition to its well-recognized role in controlling phosphate homeostasis, also regulates key metabolic processes crucial for iron-limited cyanobacteria, including ROS detoxification and iron uptake. Transcript abundances of PhoB-targeted genes are enriched in samples from phosphorus-depleted seawater, and a conserved PhoB-binding site is widely present in the promoters of the target genes, suggesting that the PhoB-mediated regulation may be highly conserved. Our findings provide molecular insights into the responses of cyanobacteria to simultaneous iron/phosphorus nutrient limitation.
Collapse
Affiliation(s)
- Guo-Wei Qiu
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Wen-Can Zheng
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Hao-Ming Yang
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Yu-Ying Wang
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Xing Qi
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Da Huang
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Guo-Zheng Dai
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Huazhong Shi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409, USA
| | - Neil M Price
- Department of Biology, McGill University, 1205 Docteur Penfield, Montreal, Québec, H3A 1B1, Canada
| | - Bao-Sheng Qiu
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China.
| |
Collapse
|
7
|
Breedt G, Korsten L, Gokul JK. Influence of Soil Phosphate on Rhizobacterial Performance in Affecting Wheat Yield. Curr Microbiol 2024; 81:170. [PMID: 38734822 PMCID: PMC11088555 DOI: 10.1007/s00284-024-03685-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 04/01/2024] [Indexed: 05/13/2024]
Abstract
As a primary nutrient in agricultural soils, phosphorus plays a crucial but growth-limiting role for plants due to its complex interactions with various soil elements. This often results in excessive phosphorus fertilizer application, posing concerns for the environment. Agri-research has therefore shifted focus to increase fertilizer-use efficiency and minimize environmental impact by leveraging plant growth-promoting rhizobacteria. This study aimed to evaluate the in-field incremental effect of inorganic phosphate concentration (up to 50 kg/ha/P) on the ability of two rhizobacterial isolates, Lysinibacillus sphaericus (T19), Paenibacillus alvei (T29), from the previous Breedt et al. (Ann Appl Biol 171:229-236, 2017) study on maize in enhancing the yield of commercially grown Duzi® cultivar wheat. Results obtained from three seasons of field trials revealed a significant relationship between soil phosphate concentration and the isolates' effectiveness in improving wheat yield. Rhizospheric samples collected at flowering during the third season, specifically to assess phosphatase enzyme activity at the different soil phosphate levels, demonstrated a significant decrease in soil phosphatase activity when the phosphorus rate reached 75% for both isolates. Furthermore, in vitro assessments of inorganic phosphate solubilization by both isolates at five increments of tricalcium phosphate-amended Pikovskaya media found that only isolate T19 was capable of solubilizing tricalcium at concentrations exceeding 3 mg/ml. The current study demonstrates the substantial influence of inorganic phosphate on the performance of individual rhizobacterial isolates, highlighting that this is an essential consideration when optimizing these isolates to increase wheat yield in commercial cultivation.
Collapse
Affiliation(s)
- Gerhardus Breedt
- Limpopo Department of Agriculture and Rural Development, Towoomba ADC, Private Bag X1615, Bela-Bela, South Africa
- Department of Plant and Soil Sciences, University of Pretoria, Private Bag X20, Pretoria, South Africa
| | - Lise Korsten
- Department of Plant and Soil Sciences, University of Pretoria, Private Bag X20, Pretoria, South Africa
- Department of Science and Innovation - National Research Foundation Centre of Excellence in Food Security, Pretoria, South Africa
| | - Jarishma Keriuscia Gokul
- Department of Plant and Soil Sciences, University of Pretoria, Private Bag X20, Pretoria, South Africa.
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Private Bag X20, Pretoria, South Africa.
| |
Collapse
|
8
|
Corrales D, Alcántara C, Clemente MJ, Vélez D, Devesa V, Monedero V, Zúñiga M. Phosphate Uptake and Its Relation to Arsenic Toxicity in Lactobacilli. Int J Mol Sci 2024; 25:5017. [PMID: 38732236 PMCID: PMC11084836 DOI: 10.3390/ijms25095017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/19/2024] [Accepted: 05/01/2024] [Indexed: 05/13/2024] Open
Abstract
The use of probiotic lactobacilli has been proposed as a strategy to mitigate damage associated with exposure to toxic metals. Their protective effect against cationic metal ions, such as those of mercury or lead, is believed to stem from their chelating and accumulating potential. However, their retention of anionic toxic metalloids, such as inorganic arsenic, is generally low. Through the construction of mutants in phosphate transporter genes (pst) in Lactiplantibacillus plantarum and Lacticaseibacillus paracasei strains, coupled with arsenate [As(V)] uptake and toxicity assays, we determined that the incorporation of As(V), which structurally resembles phosphate, is likely facilitated by phosphate transporters. Surprisingly, inactivation in Lc. paracasei of PhoP, the transcriptional regulator of the two-component system PhoPR, a signal transducer involved in phosphate sensing, led to an increased resistance to arsenite [As(III)]. In comparison to the wild type, the phoP strain exhibited no differences in the ability to retain As(III), and there were no observed changes in the oxidation of As(III) to the less toxic As(V). These results reinforce the idea that specific transport, and not unspecific cell retention, plays a role in As(V) biosorption by lactobacilli, while they reveal an unexpected phenotype for the lack of the pleiotropic regulator PhoP.
Collapse
Affiliation(s)
- Daniela Corrales
- Lactic Acid Bacteria and Probiotics Laboratory, Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Av. Agustín Escardino 7, 46980 Paterna, Spain; (D.C.); (C.A.)
| | - Cristina Alcántara
- Lactic Acid Bacteria and Probiotics Laboratory, Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Av. Agustín Escardino 7, 46980 Paterna, Spain; (D.C.); (C.A.)
| | - María Jesús Clemente
- Next-Generation Approaches for Integrative Food Toxicology Group, Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Av. Catedràtic Agustín Escardino 7, 46980 Paterna, Spain; (M.J.C.); (D.V.); (V.D.)
| | - Dinoraz Vélez
- Next-Generation Approaches for Integrative Food Toxicology Group, Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Av. Catedràtic Agustín Escardino 7, 46980 Paterna, Spain; (M.J.C.); (D.V.); (V.D.)
| | - Vicenta Devesa
- Next-Generation Approaches for Integrative Food Toxicology Group, Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Av. Catedràtic Agustín Escardino 7, 46980 Paterna, Spain; (M.J.C.); (D.V.); (V.D.)
| | - Vicente Monedero
- Lactic Acid Bacteria and Probiotics Laboratory, Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Av. Agustín Escardino 7, 46980 Paterna, Spain; (D.C.); (C.A.)
| | - Manuel Zúñiga
- Lactic Acid Bacteria and Probiotics Laboratory, Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Av. Agustín Escardino 7, 46980 Paterna, Spain; (D.C.); (C.A.)
| |
Collapse
|
9
|
Lejeune C, Cornu D, Sago L, Redeker V, Virolle MJ. The stringent response is strongly activated in the antibiotic producing strain, Streptomyces coelicolor. Res Microbiol 2024; 175:104177. [PMID: 38159786 DOI: 10.1016/j.resmic.2023.104177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 01/03/2024]
Abstract
S. lividans and S. coelicolor are phylogenetically closely related strains with different abilities to produce the same specialized metabolites. Previous studies revealed that the strong antibiotic producer, S. coelicolor, had a lower ability to assimilate nitrogen and phosphate than the weak producer, Streptomyces lividans, and this resulted into a lower growth rate. A comparative proteomic dataset was used to establish the consequences of these nutritional stresses on the abundance of proteins of the translational apparatus of these strains, grown in low and high phosphate availability. Our study revealed that most proteins of the translational apparatus were less abundant in S. coelicolor than in S. lividans whereas it was the opposite for ET-Tu 3 and a TrmA-like methyltransferase. The expression of the latter being known to be under the positive control of the stringent response whereas that of the other ribosomal proteins is under its negative control, this indicated the occurrence of a strong activation of the stringent response in S. coelicolor. Furthermore, in S. lividans, ribosomal proteins were more abundant in phosphate proficiency than in phosphate limitation suggesting that a limitation in phosphate, that was also shown to trigger RelA expression, contributes to the induction of the stringent response.
Collapse
Affiliation(s)
- Clara Lejeune
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France.
| | - David Cornu
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France.
| | - Laila Sago
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France.
| | - Virginie Redeker
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France; Institut Francois Jacob, Molecular Imaging Center (MIRCen), Laboratory of Neurodegenerative Diseases, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Centre National de la Recherche Scientifique, Université Paris-Saclay, Fontenay-aux-Roses, France.
| | - Marie-Joelle Virolle
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France.
| |
Collapse
|
10
|
Mishra S, Zhang X, Yang X. Plant communication with rhizosphere microbes can be revealed by understanding microbial functional gene composition. Microbiol Res 2024; 284:127726. [PMID: 38643524 DOI: 10.1016/j.micres.2024.127726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 03/26/2024] [Accepted: 04/12/2024] [Indexed: 04/23/2024]
Abstract
Understanding rhizosphere microbial ecology is necessary to reveal the interplay between plants and associated microbial communities. The significance of rhizosphere-microbial interactions in plant growth promotion, mediated by several key processes such as auxin synthesis, enhanced nutrient uptake, stress alleviation, disease resistance, etc., is unquestionable and well reported in numerous literature. Moreover, rhizosphere research has witnessed tremendous progress due to the integration of the metagenomics approach and further shift in our viewpoint from taxonomic to functional diversity over the past decades. The microbial functional genes corresponding to the beneficial functions provide a solid foundation for the successful establishment of positive plant-microbe interactions. The microbial functional gene composition in the rhizosphere can be regulated by several factors, e.g., the nutritional requirements of plants, soil chemistry, soil nutrient status, pathogen attack, abiotic stresses, etc. Knowing the pattern of functional gene composition in the rhizosphere can shed light on the dynamics of rhizosphere microbial ecology and the strength of cooperation between plants and associated microbes. This knowledge is crucial to realizing how microbial functions respond to unprecedented challenges which are obvious in the Anthropocene. Unraveling how microbes-mediated beneficial functions will change under the influence of several challenges, requires knowledge of the pattern and composition of functional genes corresponding to beneficial functions such as biogeochemical functions (nutrient cycle), plant growth promotion, stress mitigation, etc. Here, we focus on the molecular traits of plant growth-promoting functions delivered by a set of microbial functional genes that can be useful to the emerging field of rhizosphere functional ecology.
Collapse
Affiliation(s)
- Sandhya Mishra
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China.
| | - Xianxian Zhang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaodong Yang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China.
| |
Collapse
|
11
|
Bedoya-Pérez LP, Aguilar-Vera A, Sánchez-Pérez M, Utrilla J, Sohlenkamp C. Enhancing Escherichia coli abiotic stress resistance through ornithine lipid formation. Appl Microbiol Biotechnol 2024; 108:288. [PMID: 38587638 PMCID: PMC11001654 DOI: 10.1007/s00253-024-13130-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 02/21/2024] [Accepted: 03/27/2024] [Indexed: 04/09/2024]
Abstract
Escherichia coli is a common host for biotechnology and synthetic biology applications. During growth and fermentation, the microbes are often exposed to stress conditions, such as variations in pH or solvent concentrations. Bacterial membranes play a key role in response to abiotic stresses. Ornithine lipids (OLs) are a group of membrane lipids whose presence and synthesis have been related to stress resistance in bacteria. We wondered if this stress resistance could be transferred to bacteria not encoding the capacity to form OLs in their genome, such as E. coli. In this study, we engineered different E. coli strains to produce unmodified OLs and hydroxylated OLs by expressing the synthetic operon olsFC. Our results showed that OL formation improved pH resistance and increased biomass under phosphate limitation. Transcriptome analysis revealed that OL-forming strains differentially expressed stress- and membrane-related genes. OL-producing strains also showed better growth in the presence of the ionophore carbonyl cyanide 3-chlorophenylhydrazone (CCCP), suggesting reduced proton leakiness in OL-producing strains. Furthermore, our engineered strains showed improved heterologous violacein production at phosphate limitation and also at low pH. Overall, this study demonstrates the potential of engineering the E. coli membrane composition for constructing robust hosts with an increased abiotic stress resistance for biotechnology and synthetic biology applications. KEY POINTS: • Ornithine lipid production in E. coli increases biomass yield under phosphate limitation. • Engineered strains show an enhanced production phenotype under low pH stress. • Transcriptome analysis and CCCP experiments revealed reduced proton leakage.
Collapse
Affiliation(s)
- Leidy Patricia Bedoya-Pérez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad S/N Col. Chamilpa, C.P. 62210, Cuernavaca, Mor, México
| | - Alejandro Aguilar-Vera
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad S/N Col. Chamilpa, C.P. 62210, Cuernavaca, Mor, México
| | - Mishael Sánchez-Pérez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad S/N Col. Chamilpa, C.P. 62210, Cuernavaca, Mor, México
| | - José Utrilla
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad S/N Col. Chamilpa, C.P. 62210, Cuernavaca, Mor, México.
| | - Christian Sohlenkamp
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad S/N Col. Chamilpa, C.P. 62210, Cuernavaca, Mor, México.
| |
Collapse
|
12
|
Su H, Lai H, Gao F, Zhang R, Wu S, Ge F, Li Y, Yao H. The proliferation of beneficial bacteria influences the soil C, N, and P cycling in the soybean-maize intercropping system. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:25688-25705. [PMID: 38483720 DOI: 10.1007/s11356-024-32851-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 03/06/2024] [Indexed: 04/19/2024]
Abstract
Soybean-maize intercropping system can improve the utilization rate of farmland and the sustainability of crop production systems. However, there is a significant gap in understanding the interaction mechanisms between soil carbon (C), nitrogen (N), and phosphorus (P) cycling functional genes, rhizosphere microorganisms, and nutrient availability. To reveal the key microorganisms associated with soil nutrient utilization and C, N, and P cycling function in the soybean-maize intercropping system, we investigated the changes in soil properties, microbial community structure, and abundance of functional genes for C, N, and P cycling under soybean-maize intercropping and monocropping at different fertility stages in a pot experiment. We found that there was no significant difference in the rhizosphere microbial community between soybean-maize intercropping and monocropping at the seeding stage. As the reproductive period progressed, differences in microbial community structure between intercropping and monocropping gradually became significant, manifesting the advantages of intercropping. During the intercropping process of soybean and maize, the relative abundance of beneficial bacteria in soil rhizosphere significantly increased, particularly Streptomycetaceae and Pseudomonadaceae. Moreover, the abundances of C, N, and P cycling functional genes, such as abfA, mnp, rbcL, pmoA (C cycling), nifH, nirS-3, nosZ-2, amoB (N cycling), phoD, and ppx (P cycling), also increased significantly. Redundancy analysis and correlation analysis showed that Streptomycetaceae and Pseudomonadaceae were significantly correlated with soil properties and C, N, and P cycling functional genes. In brief, soybean and maize intercropping can change the structure of microbial community and promote the proliferation of beneficial bacteria in the soil rhizosphere. The accumulation of these beneficial bacteria increased the abundance of C, N, and P cycling functional genes in soil and enhanced the ability of plants to fully utilize environmental nutrients and promoted growth.
Collapse
Affiliation(s)
- Hao Su
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, Fujian Province, China
- Zhejiang Provincial Key Laboratory of Urban Environmental Process and Pollution Control, Ningbo (Beilun) Zhongke Haixi Industry Technology Innovation Center, Ningbo, 315800, Zhejiang Province, China
- College of JunCao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Huiling Lai
- Lianhe Equator Environmental Impact Assessment Co., Ltd, Tianjin, 300042, China
| | - Fuyun Gao
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, Fujian Province, China
- Zhejiang Provincial Key Laboratory of Urban Environmental Process and Pollution Control, Ningbo (Beilun) Zhongke Haixi Industry Technology Innovation Center, Ningbo, 315800, Zhejiang Province, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ruipeng Zhang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, Fujian Province, China
- Zhejiang Provincial Key Laboratory of Urban Environmental Process and Pollution Control, Ningbo (Beilun) Zhongke Haixi Industry Technology Innovation Center, Ningbo, 315800, Zhejiang Province, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sixuan Wu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, Fujian Province, China
- Zhejiang Provincial Key Laboratory of Urban Environmental Process and Pollution Control, Ningbo (Beilun) Zhongke Haixi Industry Technology Innovation Center, Ningbo, 315800, Zhejiang Province, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Furong Ge
- Beilun District Agriculture and Rural Bureau, Ningbo, 315800, Zhejiang Province, China
| | - Yaying Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, Fujian Province, China.
- Zhejiang Provincial Key Laboratory of Urban Environmental Process and Pollution Control, Ningbo (Beilun) Zhongke Haixi Industry Technology Innovation Center, Ningbo, 315800, Zhejiang Province, China.
| | - Huaiying Yao
- Wuhan Institute of Technology, Wuhan, 430074, China
| |
Collapse
|
13
|
Santos‐Beneit F. What is the role of microbial biotechnology and genetic engineering in medicine? Microbiologyopen 2024; 13:e1406. [PMID: 38556942 PMCID: PMC10982607 DOI: 10.1002/mbo3.1406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/26/2024] [Accepted: 03/12/2024] [Indexed: 04/02/2024] Open
Abstract
Microbial products are essential for developing various therapeutic agents, including antibiotics, anticancer drugs, vaccines, and therapeutic enzymes. Genetic engineering techniques, functional genomics, and synthetic biology unlock previously uncharacterized natural products. This review highlights major advances in microbial biotechnology, focusing on gene-based technologies for medical applications.
Collapse
Affiliation(s)
- Fernando Santos‐Beneit
- Institute of Sustainable ProcessesValladolidSpain
- Department of Chemical Engineering and Environmental Technology, School of Industrial EngineeringUniversity of ValladolidValladolidSpain
| |
Collapse
|
14
|
Zouagui R, Zouagui H, Aurag J, Ibrahimi A, Sbabou L. Functional analysis and comparative genomics of Rahnella perminowiae S11P1 and Variovorax sp. S12S4, two plant growth-promoting rhizobacteria isolated from Crocus sativus L. (saffron) rhizosphere. BMC Genomics 2024; 25:289. [PMID: 38500021 PMCID: PMC10946135 DOI: 10.1186/s12864-024-10088-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 02/03/2024] [Indexed: 03/20/2024] Open
Abstract
BACKGROUND Rahnella perminowiae S11P1 and Variovorax sp. S12S4 are two plant growth-promoting rhizobacteria that were previously isolated from the rhizosphere of Crocus sativus L. (saffron), and have demonstrated interesting PGP activities and promising results when used as inoculants in field trials. To further elucidate the molecular mechanisms underlying their beneficial effects on plant growth, comprehensive genome mining of S11P1 and S12S4 and comparative genomic analysis with closely related strains were conducted. RESULTS Functional annotation of the two strains predicted a large number of genes involved in auxin and siderophore production, nitrogen fixation, sulfur metabolism, organic acid biosynthesis, pyrroloquinoline quinone production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, volatile organic compounds production, and polyamine biosynthesis. In addition, numerous genes implicated in plant-bacteria interactions, such as those involved in chemotaxis and quorum sensing, were predicted. Moreover, the two strains carried genes involved in bacterial fitness under abiotic stress conditions. Comparative genomic analysis revealed an open pan-genomic structure for the two strains. COG annotation showed that higher fractions of core and accessory genes were involved in the metabolism and transport of carbohydrates and amino acids, suggesting the metabolic versatility of the two strains as effective rhizosphere colonizers. Furthermore, this study reports the first comparison of Multilocus sequence analysis (MLSA) and core-based phylogenies of the Rahnella and Variovorax genera. CONCLUSIONS The present study unveils the molecular mechanisms underlying plant growth promotion and biocontrol activity of S11P1 and S12S4, and provides a basis for their further biotechnological application in agriculture.
Collapse
Affiliation(s)
- Rahma Zouagui
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco
| | - Houda Zouagui
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco
- Biotechnology Lab (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University in Rabat, Rabat, Morocco
| | - Jamal Aurag
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco
| | - Azeddine Ibrahimi
- Biotechnology Lab (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University in Rabat, Rabat, Morocco
| | - Laila Sbabou
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco.
| |
Collapse
|
15
|
Lidbury IDEA, Hitchcock A, Groenhof SRM, Connolly AN, Moushtaq L. New insights in bacterial organophosphorus cycling: From human pathogens to environmental bacteria. Adv Microb Physiol 2024; 84:1-49. [PMID: 38821631 DOI: 10.1016/bs.ampbs.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2024]
Abstract
In terrestrial and aquatic ecosystems, phosphorus (P) availability controls primary production, with consequences for climate regulation and global food security. Understanding the microbial controls on the global P cycle is a prerequisite for minimising our reliance on non-renewable phosphate rock reserves and reducing pollution associated with excessive P fertiliser use. This recognised importance has reinvigorated research into microbial P cycling, which was pioneered over 75 years ago through the study of human pathogenic bacteria-host interactions. Immobilised organic P represents a significant fraction of the total P pool. Hence, microbes have evolved a plethora of mechanisms to transform this fraction into labile inorganic phosphate, the building block for numerous biological molecules. The 'genomics era' has revealed an extraordinary diversity of organic P cycling genes exist in the environment and studies going 'back to the lab' are determining how this diversity relates to function. Through this integrated approach, many hitherto unknown genes and proteins that are involved in microbial P cycling have been discovered. Not only do these fundamental discoveries push the frontier of our knowledge, but several examples also provide exciting opportunities for biotechnology and present possible solutions for improving the sustainability of how we grow our food, both locally and globally. In this review, we provide a comprehensive overview of bacterial organic P cycling, covering studies on human pathogens and how this knowledge is informing new discoveries in environmental microbiology.
Collapse
Affiliation(s)
- Ian D E A Lidbury
- Molecular Microbiology - Biochemistry and Disease, School of Biosciences, The University of Sheffield, Sheffield, United Kingdom.
| | - Andrew Hitchcock
- Molecular Microbiology - Biochemistry and Disease, School of Biosciences, The University of Sheffield, Sheffield, United Kingdom; Plants, Photosynthesis, and Soil, School of Biosciences, The University of Sheffield, Sheffield, United Kingdom
| | - Sophie R M Groenhof
- Molecular Microbiology - Biochemistry and Disease, School of Biosciences, The University of Sheffield, Sheffield, United Kingdom
| | - Alex N Connolly
- Molecular Microbiology - Biochemistry and Disease, School of Biosciences, The University of Sheffield, Sheffield, United Kingdom
| | - Laila Moushtaq
- Molecular Microbiology - Biochemistry and Disease, School of Biosciences, The University of Sheffield, Sheffield, United Kingdom
| |
Collapse
|
16
|
Fabian B, Foster C, Asher A, Hassan K, Paulsen I, Tetu S. Identifying the suite of genes central to swimming in the biocontrol bacterium Pseudomonas protegens Pf-5. Microb Genom 2024; 10:001212. [PMID: 38546328 PMCID: PMC11004494 DOI: 10.1099/mgen.0.001212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 02/20/2024] [Indexed: 04/12/2024] Open
Abstract
Swimming motility is a key bacterial trait, important to success in many niches. Biocontrol bacteria, such as Pseudomonas protegens Pf-5, are increasingly used in agriculture to control crop diseases, where motility is important for colonization of the plant rhizosphere. Swimming motility typically involves a suite of flagella and chemotaxis genes, but the specific gene set employed for both regulation and biogenesis can differ substantially between organisms. Here we used transposon-directed insertion site sequencing (TraDIS), a genome-wide approach, to identify 249 genes involved in P. protegens Pf-5 swimming motility. In addition to the expected flagella and chemotaxis, we also identified a suite of additional genes important for swimming, including genes related to peptidoglycan turnover, O-antigen biosynthesis, cell division, signal transduction, c-di-GMP turnover and phosphate transport, and 27 conserved hypothetical proteins. Gene knockout mutants and TraDIS data suggest that defects in the Pst phosphate transport system lead to enhanced swimming motility. Overall, this study expands our knowledge of pseudomonad motility and highlights the utility of a TraDIS-based approach for analysing the functions of thousands of genes. This work sets a foundation for understanding how swimming motility may be related to the inconsistency in biocontrol bacteria performance in the field.
Collapse
Affiliation(s)
- B.K. Fabian
- School of Natural Sciences, Macquarie University, Sydney, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - C. Foster
- School of Natural Sciences, Macquarie University, Sydney, Australia
| | - A. Asher
- School of Natural Sciences, Macquarie University, Sydney, Australia
| | - K.A. Hassan
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
- School of Environmental and Life Sciences, University of Newcastle, Newcastle, Australia
| | - I.T. Paulsen
- School of Natural Sciences, Macquarie University, Sydney, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - S.G. Tetu
- School of Natural Sciences, Macquarie University, Sydney, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| |
Collapse
|
17
|
Duport C, Armengaud J, Schmitt C, Morin D, Lacapère JJ. Elucidating the pivotal role of TSPO in porphyrin-related cellular processes, in Bacillus cereus. Biochimie 2024:S0300-9084(24)00046-4. [PMID: 38423451 DOI: 10.1016/j.biochi.2024.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 03/02/2024]
Abstract
A structural homolog of the mammalian TSPO has been identified in the human pathogen Bacillus cereus. BcTSPO, in its recombinant form, has previously been shown to bind and degrade porphyrins. In this study, we generated a ΔtspO mutant strain in B. cereus ATCC 14579 and assessed the impact of the absence of BcTSPO on cellular proteomics and physiological characteristics. The proteomic analysis revealed correlations between the lack of BcTSPO and the observed growth defects, increased oxygen consumption, ATP deficiency, heightened tryptophan catabolism, reduced motility, and impaired biofilm formation in the ΔtspO mutant strain. Our results also suggested that BcTSPO plays a crucial role in regulating intracellular levels of metabolites from the coproporphyrin-dependent branch of the heme biosynthetic pathway. This regulation potentially underlies alterations in the metabolic landscape, emphasizing the pivotal role of BcTSPO in B. cereus aerobic metabolism. Notably, our study unveils, for the first time, the involvement of TSPO in tryptophan metabolism. These findings underscore the multifaceted role of TSPO, not only in metabolic pathways but also potentially in the microorganism's virulence mechanisms.
Collapse
Affiliation(s)
| | - Jean Armengaud
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200, Bagnols-sur-Cèze, France
| | - Caroline Schmitt
- Assistance Publique Hôpitaux de Paris (AP-HP), Centre Français des Porphyries, Hôpital Louis Mourier, 92700, Colombes, France; INSERM U1149, Center for Research on Inflammation (CRI), Université de Paris, 75018, Paris, France
| | - Didier Morin
- INSERM, U955, équipe 3, Faculté de Médecine, Université Paris Est, 94010, Creteil, France
| | - Jean-Jacques Lacapère
- Sorbonne Université, Ecole Normale Supérieure, PSL University, CNRS UMR 7203, Laboratoire des BioMolécules (LBM), 4 place Jussieu, F-75005, Paris, France
| |
Collapse
|
18
|
Menon ND, Poudel S, Sastry AV, Rychel K, Szubin R, Dillon N, Tsunemoto H, Hirose Y, Nair BG, Kumar GB, Palsson BO, Nizet V. Independent component analysis reveals 49 independently modulated gene sets within the global transcriptional regulatory architecture of multidrug-resistant Acinetobacter baumannii. mSystems 2024; 9:e0060623. [PMID: 38189271 PMCID: PMC10878099 DOI: 10.1128/msystems.00606-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 11/29/2023] [Indexed: 01/09/2024] Open
Abstract
Acinetobacter baumannii causes severe infections in humans, resists multiple antibiotics, and survives in stressful environmental conditions due to modulations of its complex transcriptional regulatory network (TRN). Unfortunately, our global understanding of the TRN in this emerging opportunistic pathogen is limited. Here, we apply independent component analysis, an unsupervised machine learning method, to a compendium of 139 RNA-seq data sets of three multidrug-resistant A. baumannii international clonal complex I strains (AB5075, AYE, and AB0057). This analysis allows us to define 49 independently modulated gene sets, which we call iModulons. Analysis of the identified A. baumannii iModulons reveals validating parallels to previously defined biological operons/regulons and provides a framework for defining unknown regulons. By utilizing the iModulons, we uncover potential mechanisms for a RpoS-independent general stress response, define global stress-virulence trade-offs, and identify conditions that may induce plasmid-borne multidrug resistance. The iModulons provide a model of the TRN that emphasizes the importance of transcriptional regulation of virulence phenotypes in A. baumannii. Furthermore, they suggest the possibility of future interventions to guide gene expression toward diminished pathogenic potential.IMPORTANCEThe rise in hospital outbreaks of multidrug-resistant Acinetobacter baumannii infections underscores the urgent need for alternatives to traditional broad-spectrum antibiotic therapies. The success of A. baumannii as a significant nosocomial pathogen is largely attributed to its ability to resist antibiotics and survive environmental stressors. However, there is limited literature available on the global, complex regulatory circuitry that shapes these phenotypes. Computational tools that can assist in the elucidation of A. baumannii's transcriptional regulatory network architecture can provide much-needed context for a comprehensive understanding of pathogenesis and virulence, as well as for the development of targeted therapies that modulate these pathways.
Collapse
Affiliation(s)
- Nitasha D. Menon
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Kerala, India
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Saugat Poudel
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Anand V. Sastry
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Kevin Rychel
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Richard Szubin
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Nicholas Dillon
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
- Department of Biological Sciences, University of Texas at Dallas, Dallas, Texas, USA
| | - Hannah Tsunemoto
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Yujiro Hirose
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
- Department of Microbiology, Graduate School of Dentistry, Osaka University, Suita, Osaka, Japan
| | - Bipin G. Nair
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Kerala, India
| | - Geetha B. Kumar
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Kerala, India
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Victor Nizet
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
| |
Collapse
|
19
|
Voutsinos MY, West-Roberts JA, Sachdeva R, Moreau JW, Banfield JF. Weathered granites and soils harbour microbes with lanthanide-dependent methylotrophic enzymes. BMC Biol 2024; 22:41. [PMID: 38369453 PMCID: PMC10875860 DOI: 10.1186/s12915-024-01841-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 02/07/2024] [Indexed: 02/20/2024] Open
Abstract
BACKGROUND Prior to soil formation, phosphate liberated by rock weathering is often sequestered into highly insoluble lanthanide phosphate minerals. Dissolution of these minerals releases phosphate and lanthanides to the biosphere. Currently, the microorganisms involved in phosphate mineral dissolution and the role of lanthanides in microbial metabolism are poorly understood. RESULTS Although there have been many studies of soil microbiology, very little research has investigated microbiomes of weathered rock. Here, we sampled weathered granite and associated soil to identify the zones of lanthanide phosphate mineral solubilisation and genomically define the organisms implicated in lanthanide utilisation. We reconstructed 136 genomes from 11 bacterial phyla and found that gene clusters implicated in lanthanide-based metabolism of methanol (primarily xoxF3 and xoxF5) are surprisingly common in microbial communities in moderately weathered granite. Notably, xoxF3 systems were found in Verrucomicrobia for the first time, and in Acidobacteria, Gemmatimonadetes and Alphaproteobacteria. The xoxF-containing gene clusters are shared by diverse Acidobacteria and Gemmatimonadetes, and include conserved hypothetical proteins and transporters not associated with the few well studied xoxF systems. Given that siderophore-like molecules that strongly bind lanthanides may be required to solubilise lanthanide phosphates, it is notable that candidate metallophore biosynthesis systems were most prevalent in bacteria in moderately weathered rock, especially in Acidobacteria with lanthanide-based systems. CONCLUSIONS Phosphate mineral dissolution, putative metallophore production and lanthanide utilisation by enzymes involved in methanol oxidation linked to carbonic acid production co-occur in the zone of moderate granite weathering. In combination, these microbial processes likely accelerate the conversion of granitic rock to soil.
Collapse
Affiliation(s)
- Marcos Y Voutsinos
- School of Geography, Earth and Atmospheric Sciences, The University of Melbourne, Melbourne, VIC, Australia
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Jacob A West-Roberts
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
| | - Rohan Sachdeva
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | - John W Moreau
- School of Geographical and Earth Sciences, University of Glasgow, Glasgow, UK
| | - Jillian F Banfield
- School of Geography, Earth and Atmospheric Sciences, The University of Melbourne, Melbourne, VIC, Australia.
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia.
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA.
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA.
| |
Collapse
|
20
|
Acosta-Zaldívar M, Qi W, Mishra A, Roy U, King WR, Patton-Vogt J, Anderson MZ, Köhler JR. Candida albicans' inorganic phosphate transport and evolutionary adaptation to phosphate scarcity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.29.577887. [PMID: 38352318 PMCID: PMC10862840 DOI: 10.1101/2024.01.29.577887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Phosphorus is essential in all cells' structural, metabolic and regulatory functions. For fungal cells that import inorganic phosphate (Pi) up a steep concentration gradient, surface Pi transporters are critical capacitators of growth. Fungi must deploy Pi transporters that enable optimal Pi uptake in pH and Pi concentration ranges prevalent in their environments. Single, triple and quadruple mutants were used to characterize the four Pi transporters we identified for the human fungal pathogen Candida albicans, which must adapt to alkaline conditions during invasion of the host bloodstream and deep organs. A high-affinity Pi transporter, Pho84, was most efficient across the widest pH range while another, Pho89, showed high-affinity characteristics only within one pH unit of neutral. Two low-affinity Pi transporters, Pho87 and Fgr2, were active only in acidic conditions. Only Pho84 among the Pi transporters was clearly required in previously identified Pi-related functions including Target of Rapamycin Complex 1 signaling and hyphal growth. We used in vitro evolution and whole genome sequencing as an unbiased forward genetic approach to probe adaptation to prolonged Pi scarcity of two quadruple mutant lineages lacking all 4 Pi transporters. Lineage-specific genomic changes corresponded to divergent success of the two lineages in fitness recovery during Pi limitation. In this process, initial, large-scale genomic alterations like aneuploidies and loss of heterozygosity were eventually lost as populations presumably gained small-scale mutations. Severity of some phenotypes linked to Pi starvation, like cell wall stress hypersensitivity, decreased in parallel to evolving populations' fitness recovery in Pi scarcity, while that of others like membrane stress responses diverged from these fitness phenotypes. C. albicans therefore has diverse options to reconfigure Pi management during prolonged scarcity. Since Pi homeostasis differs substantially between fungi and humans, adaptive processes to Pi deprivation may harbor small-molecule targets that impact fungal growth and virulence.
Collapse
Affiliation(s)
- Maikel Acosta-Zaldívar
- Division of Infectious Diseases, Boston Children’s Hospital/Harvard Medical School, Boston, MA 02115, USA
- Current affiliation: Planasa, Valladolid, Spain
| | - Wanjun Qi
- Division of Infectious Diseases, Boston Children’s Hospital/Harvard Medical School, Boston, MA 02115, USA
| | - Abhishek Mishra
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI
| | - Udita Roy
- Division of Infectious Diseases, Boston Children’s Hospital/Harvard Medical School, Boston, MA 02115, USA
| | - William R. King
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA
| | - Jana Patton-Vogt
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA
| | - Matthew Z. Anderson
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI
- Department of Medical Genetics, Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI
| | - Julia R. Köhler
- Division of Infectious Diseases, Boston Children’s Hospital/Harvard Medical School, Boston, MA 02115, USA
| |
Collapse
|
21
|
Skoog EJ, Bosak T. Predicted metabolic roles and stress responses provide insights into candidate phyla Hydrogenedentota and Sumerlaeota as members of the rare biosphere in biofilms from various environments. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13228. [PMID: 38192240 PMCID: PMC10866078 DOI: 10.1111/1758-2229.13228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 12/11/2023] [Indexed: 01/10/2024]
Abstract
Pustular mats from Shark Bay, Western Australia, host complex microbial communities bound within an organic matrix. These mats harbour many poorly characterized organisms with low relative abundances (<1%), such as candidate phyla Hydrogenedentota and Sumerlaeota. Here, we aim to constrain the metabolism and physiology of these candidate phyla by analyzing two representative metagenome-assembled genomes (MAGs) from a pustular mat. Metabolic reconstructions of these MAGs suggest facultatively anaerobic, chemoorganotrophic lifestyles of both organisms and predict that both MAGs can metabolize a diversity of carbohydrate substrates. Ca. Sumerlaeota possesses genes involved in degrading chitin, cellulose and other polysaccharides, while Ca. Hydrogenedentota can metabolize cellulose derivatives in addition to glycerol, fatty acids and phosphonates. Both Ca. phyla can respond to nitrosative stress and participate in nitrogen metabolism. Metabolic comparisons of MAGs from Shark Bay and those from various polyextreme environments (i.e., hot springs, hydrothermal vents, subsurface waters, anaerobic digesters, etc.) reveal similar metabolic capabilities and adaptations to hypersalinity, oxidative stress, antibiotics, UV radiation, nitrosative stress, heavy metal toxicity and life in surface-attached communities. These adaptations and capabilities may account for the widespread nature of these organisms and their contributions to biofilm communities in a range of extreme surface and subsurface environments.
Collapse
Affiliation(s)
- Emilie J. Skoog
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
- Integrative Oceanography DivisionScripps Institution of Oceanography, UC San DiegoLa JollaCaliforniaUSA
| | - Tanja Bosak
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| |
Collapse
|
22
|
He C, Wu H, Wei G, Zhu S, Qiu G, Wei C. Simultaneous decarbonization and phosphorus removal by Tetrasphaera elongata with glucose as carbon source under aerobic conditions. BIORESOURCE TECHNOLOGY 2024; 393:130048. [PMID: 37980947 DOI: 10.1016/j.biortech.2023.130048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 11/04/2023] [Accepted: 11/15/2023] [Indexed: 11/21/2023]
Abstract
Previous researches have recognized the vital role of Tetrasphaera elongata in enhanced biological phosphorus removal systems, but the underlying mechanisms remain under-investigated. To address this issue, this study investigated the metabolic characteristics of Tetrasphaera elongata when utilizing glucose as the sole carbon source. Results showed under aerobic conditions, Tetrasphaera elongata exhibited a glucose uptake rate of 136.6 mg/(L·h) and a corresponding phosphorus removal rate of 8.6 mg P/(L·h). Upregulations of genes associated with the glycolytic pathway and oxidative phosphorylation were observed. Noteworthily, the genes encoding the two-component sensor histidine kinase and response regulator transcription factor exhibited a remarkable 28.3 and 27.4-fold increase compared with the group without glucose. Since these genes play a pivotal role in phosphate-specific transport systems, collectively, these findings shed light on a potential mechanism for simultaneous decarbonization and phosphorus removal by Tetrasphaera elongata under aerobic conditions, providing fresh insights into phosphorus removal from wastewaters.
Collapse
Affiliation(s)
- Chao He
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Haizhen Wu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China.
| | - Gengrui Wei
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China
| | - Shuang Zhu
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
| | - Guanglei Qiu
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China
| | - Chaohai Wei
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China
| |
Collapse
|
23
|
Larsson EM, Murray RM, Newman DK. Engineering the Soil Bacterium Pseudomonas synxantha 2-79 into a Ratiometric Bioreporter for Phosphorus Limitation. ACS Synth Biol 2024; 13:384-393. [PMID: 38165130 DOI: 10.1021/acssynbio.3c00642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Microbial bioreporters hold promise for addressing challenges in medical and environmental applications. However, the difficulty in ensuring their stable persistence and function within the target environment remains a challenge. One strategy is to integrate information about the host strain and target environment into the design-build-test cycle of the bioreporter itself. Here, we present a case study for such an environmentally motivated design process by engineering the wheat commensal bacterium Pseudomonas synxantha 2-79 into a ratiometric bioreporter for phosphorus limitation. Comparative analysis showed that an exogenous P-responsive promoter outperformed its native counterparts. This reporter can selectively sense and report phosphorus limitation at plant-relevant concentrations of 25-100 μM without cross-activation from carbon or nitrogen limitation or high cell densities. Its performance is robust over a field-relevant pH range (5.8-8), and it responds only to inorganic phosphorus, even in the presence of common soil organic P. Finally, we used fluorescein-calibrated flow cytometry to assess whether the reporter's performance in shaken liquid culture predicts its performance in soil, finding that although the reporter is still functional at the bulk level, its variability in performance increases when grown in a soil slurry as compared to planktonic culture, with a fraction of the population not expressing the reporter proteins. Together, our environmentally aware design process provides an example of how laboratory bioengineering efforts can generate microbes with a greater promise to function reliably in their applied contexts.
Collapse
Affiliation(s)
- Elin M Larsson
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Richard M Murray
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, California 91125, United States
- Control and Dynamical Systems, California Institute of Technology, Pasadena, California 91125, United States
| | - Dianne K Newman
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, California 91125, United States
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California 91125, United States
| |
Collapse
|
24
|
Howard-Varona C, Lindback MM, Fudyma JD, Krongauz A, Solonenko NE, Zayed AA, Andreopoulos WB, Olson HM, Kim YM, Kyle JE, Glavina del Rio T, Adkins JN, Tfaily MM, Paul S, Sullivan MB, Duhaime MB. Environment-specific virocell metabolic reprogramming. THE ISME JOURNAL 2024; 18:wrae055. [PMID: 38552150 PMCID: PMC11170926 DOI: 10.1093/ismejo/wrae055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/23/2023] [Accepted: 03/28/2024] [Indexed: 06/14/2024]
Abstract
Viruses impact microbial systems through killing hosts, horizontal gene transfer, and altering cellular metabolism, consequently impacting nutrient cycles. A virus-infected cell, a "virocell," is distinct from its uninfected sister cell as the virus commandeers cellular machinery to produce viruses rather than replicate cells. Problematically, virocell responses to the nutrient-limited conditions that abound in nature are poorly understood. Here we used a systems biology approach to investigate virocell metabolic reprogramming under nutrient limitation. Using transcriptomics, proteomics, lipidomics, and endo- and exo-metabolomics, we assessed how low phosphate (low-P) conditions impacted virocells of a marine Pseudoalteromonas host when independently infected by two unrelated phages (HP1 and HS2). With the combined stresses of infection and nutrient limitation, a set of nested responses were observed. First, low-P imposed common cellular responses on all cells (virocells and uninfected cells), including activating the canonical P-stress response, and decreasing transcription, translation, and extracellular organic matter consumption. Second, low-P imposed infection-specific responses (for both virocells), including enhancing nitrogen assimilation and fatty acid degradation, and decreasing extracellular lipid relative abundance. Third, low-P suggested virocell-specific strategies. Specifically, HS2-virocells regulated gene expression by increasing transcription and ribosomal protein production, whereas HP1-virocells accumulated host proteins, decreased extracellular peptide relative abundance, and invested in broader energy and resource acquisition. These results suggest that although environmental conditions shape metabolism in common ways regardless of infection, virocell-specific strategies exist to support viral replication during nutrient limitation, and a framework now exists for identifying metabolic strategies of nutrient-limited virocells in nature.
Collapse
Affiliation(s)
- Cristina Howard-Varona
- Department of Microbiology, The Ohio State University, 484 W 12th Ave, Columbus, OH 43210, United States
| | - Morgan M Lindback
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Ave, Ann Arbor, MI 48109, United States
| | - Jane D Fudyma
- Department of Environmental Science, University of Arizona, 1177 E 4th St, Tucson, AZ 85719, United States
- Present address: Department of Plant Pathology, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Azriel Krongauz
- Department of Statistics, The Ohio State University, 1958 Neil Ave, Columbus, OH 43210, United States
| | - Natalie E Solonenko
- Department of Microbiology, The Ohio State University, 484 W 12th Ave, Columbus, OH 43210, United States
| | - Ahmed A Zayed
- Department of Microbiology, The Ohio State University, 484 W 12th Ave, Columbus, OH 43210, United States
| | - William B Andreopoulos
- US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA 94720, United States
- Present address: Department of Computer Science, San Jose State University, One Washington Square, San Jose CA 95192, United States
| | - Heather M Olson
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99354, United States
| | - Young-Mo Kim
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99354, United States
| | - Jennifer E Kyle
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99354, United States
| | - Tijana Glavina del Rio
- US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA 94720, United States
| | - Joshua N Adkins
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99354, United States
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR 97239, United States
| | - Malak M Tfaily
- Department of Environmental Science, University of Arizona, 1177 E 4th St, Tucson, AZ 85719, United States
| | - Subhadeep Paul
- Department of Statistics, The Ohio State University, 1958 Neil Ave, Columbus, OH 43210, United States
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, 484 W 12th Ave, Columbus, OH 43210, United States
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, 2070 Neil Ave, Columbus, OH 43210, United States
- Center for RNA Biology and Center of Microbiome Science, The Ohio State University, 484 W. 12th Ave, Columbus, OH 43210, United States
| | - Melissa B Duhaime
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Ave, Ann Arbor, MI 48109, United States
| |
Collapse
|
25
|
Rihtman B, Torcello-Requena A, Mikhaylina A, Puxty RJ, Clokie MRJ, Millard AD, Scanlan DJ. Coordinated transcriptional response to environmental stress by a Synechococcus virus. THE ISME JOURNAL 2024; 18:wrae032. [PMID: 38431846 PMCID: PMC10976474 DOI: 10.1093/ismejo/wrae032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 12/20/2023] [Accepted: 02/26/2024] [Indexed: 03/05/2024]
Abstract
Viruses are a major control on populations of microbes. Often, their virulence is examined in controlled laboratory conditions. Yet, in nature, environmental conditions lead to changes in host physiology and fitness that may impart both costs and benefits on viral success. Phosphorus (P) is a major abiotic control on the marine cyanobacterium Synechococcus. Some viruses infecting Synechococcus have acquired, from their host, a gene encoding a P substrate binding protein (PstS), thought to improve virus replication under phosphate starvation. Yet, pstS is uncommon among cyanobacterial viruses. Thus, we asked how infections with viruses lacking PstS are affected by P scarcity. We show that the production of infectious virus particles of such viruses is reduced in low P conditions. However, this reduction in progeny is not caused by impaired phage genome replication, thought to be a major sink for cellular phosphate. Instead, transcriptomic analysis showed that under low P conditions, a PstS-lacking cyanophage increased the expression of a specific gene set that included mazG, hli2, and gp43 encoding a pyrophosphatase, a high-light inducible protein and DNA polymerase, respectively. Moreover, several of the upregulated genes were controlled by the host's phoBR two-component system. We hypothesize that recycling and polymerization of nucleotides liberates free phosphate and thus allows viral morphogenesis, albeit at lower rates than when phosphate is replete or when phages encode pstS. Altogether, our data show how phage genomes, lacking obvious P-stress-related genes, have evolved to exploit their host's environmental sensing mechanisms to coordinate their own gene expression in response to resource limitation.
Collapse
Affiliation(s)
- Branko Rihtman
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Alberto Torcello-Requena
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Alevtina Mikhaylina
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Richard J Puxty
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Martha R J Clokie
- Leicester Centre for Phage Research, Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
| | - Andrew D Millard
- Leicester Centre for Phage Research, Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
| | - David J Scanlan
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| |
Collapse
|
26
|
Molina-Pardines C, Haro-Moreno JM, López-Pérez M. Phosphate-related genomic islands as drivers of environmental adaptation in the streamlined marine alphaproteobacterial HIMB59. mSystems 2023; 8:e0089823. [PMID: 38054740 PMCID: PMC10734472 DOI: 10.1128/msystems.00898-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 10/17/2023] [Indexed: 12/07/2023] Open
Abstract
IMPORTANCE These results shed light on the evolutionary strategies of microbes with streamlined genomes to adapt and survive in the oligotrophic conditions that dominate the surface waters of the global ocean. At the individual level, these microbes have been subjected to evolutionary constraints that have led to a more efficient use of nutrients, removing non-essential genes named as "streamlining theory." However, at the population level, they conserve a highly diverse gene pool in flexible genomic islands resulting in polyclonal populations on the same genomic background as an evolutionary response to environmental pressures. Localization of these islands at equivalent positions in the genome facilitates horizontal transfer between clonal lineages. This high level of environmental genomic heterogeneity could explain their cosmopolitan distribution. In the case of the order HIMB59 within the class Alphaproteobacteria, two factors exert evolutionary pressure and determine this intraspecific diversity: phages and the concentration of P in the environment.
Collapse
Affiliation(s)
- Carmen Molina-Pardines
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, San Juan, Alicante, Spain
| | - Jose M. Haro-Moreno
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, San Juan, Alicante, Spain
| | - Mario López-Pérez
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, San Juan, Alicante, Spain
| |
Collapse
|
27
|
Vannier N, Mesny F, Getzke F, Chesneau G, Dethier L, Ordon J, Thiergart T, Hacquard S. Genome-resolved metatranscriptomics reveals conserved root colonization determinants in a synthetic microbiota. Nat Commun 2023; 14:8274. [PMID: 38092730 PMCID: PMC10719396 DOI: 10.1038/s41467-023-43688-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 11/16/2023] [Indexed: 12/17/2023] Open
Abstract
The identification of processes activated by specific microbes during microbiota colonization of plant roots has been hampered by technical constraints in metatranscriptomics. These include lack of reference genomes, high representation of host or microbial rRNA sequences in datasets, or difficulty to experimentally validate gene functions. Here, we recolonized germ-free Arabidopsis thaliana with a synthetic, yet representative root microbiota comprising 106 genome-sequenced bacterial and fungal isolates. We used multi-kingdom rRNA depletion, deep RNA-sequencing and read mapping against reference microbial genomes to analyse the in planta metatranscriptome of abundant colonizers. We identified over 3,000 microbial genes that were differentially regulated at the soil-root interface. Translation and energy production processes were consistently activated in planta, and their induction correlated with bacterial strains' abundance in roots. Finally, we used targeted mutagenesis to show that several genes consistently induced by multiple bacteria are required for root colonization in one of the abundant bacterial strains (a genetically tractable Rhodanobacter). Our results indicate that microbiota members activate strain-specific processes but also common gene sets to colonize plant roots.
Collapse
Affiliation(s)
- Nathan Vannier
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
| | - Fantin Mesny
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- Institute for Plant Sciences, University of Cologne, 50923, Cologne, Germany
| | - Felix Getzke
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Guillaume Chesneau
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Laura Dethier
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Jana Ordon
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Thorsten Thiergart
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Stéphane Hacquard
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany.
- Cluster of Excellence on Plant Sciences, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany.
| |
Collapse
|
28
|
Miano A, Rychel K, Lezia A, Sastry A, Palsson B, Hasty J. High-resolution temporal profiling of E. coli transcriptional response. Nat Commun 2023; 14:7606. [PMID: 37993418 PMCID: PMC10665441 DOI: 10.1038/s41467-023-43173-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 11/02/2023] [Indexed: 11/24/2023] Open
Abstract
Understanding how cells dynamically adapt to their environment is a primary focus of biology research. Temporal information about cellular behavior is often limited by both small numbers of data time-points and the methods used to analyze this data. Here, we apply unsupervised machine learning to a data set containing the activity of 1805 native promoters in E. coli measured every 10 minutes in a high-throughput microfluidic device via fluorescence time-lapse microscopy. Specifically, this data set reveals E. coli transcriptome dynamics when exposed to different heavy metal ions. We use a bioinformatics pipeline based on Independent Component Analysis (ICA) to generate insights and hypotheses from this data. We discovered three primary, time-dependent stages of promoter activation to heavy metal stress (fast, intermediate, and steady). Furthermore, we uncovered a global strategy E. coli uses to reallocate resources from stress-related promoters to growth-related promoters following exposure to heavy metal stress.
Collapse
Affiliation(s)
- Arianna Miano
- Department of Bioengineering, University of California San Diego, 9500 Gliman Dr, La Jolla, CA, USA.
| | - Kevin Rychel
- Department of Bioengineering, University of California San Diego, 9500 Gliman Dr, La Jolla, CA, USA
| | - Andrew Lezia
- Department of Bioengineering, University of California San Diego, 9500 Gliman Dr, La Jolla, CA, USA
| | - Anand Sastry
- Department of Bioengineering, University of California San Diego, 9500 Gliman Dr, La Jolla, CA, USA
| | - Bernhard Palsson
- Department of Bioengineering, University of California San Diego, 9500 Gliman Dr, La Jolla, CA, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs, Lyngby, Denmark
| | - Jeff Hasty
- Department of Bioengineering, University of California San Diego, 9500 Gliman Dr, La Jolla, CA, USA
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, 9500 Gliman Dr, La Jolla, CA, USA
- Synthetic Biology Institute, University of California San Diego, 9500 Gliman Dr, La Jolla, CA, USA
| |
Collapse
|
29
|
Smirnova GV, Tyulenev AV, Bezmaternykh KV, Muzyka NG, Ushakov VY, Oktyabrsky ON. Phosphate starvation is accompanied by disturbance of intracellular cysteine homeostasis in Escherichia coli. Res Microbiol 2023; 174:104108. [PMID: 37516155 DOI: 10.1016/j.resmic.2023.104108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/19/2023] [Accepted: 07/24/2023] [Indexed: 07/31/2023]
Abstract
Metabolic rearrangements that occur during depletion of essential nutrients can lead to accumulation of potentially dangerous metabolites. Here we showed that depletion of phosphate (Pi), accompanied by a sharp inhibition of growth and respiration, caused a transient excess of intracellular cysteine due to a decrease in the rate of protein synthesis. High cysteine level can be dangerous due to its ability to produce ROS and reduce Fe3+ to Fenton-reactive Fe2+. To prevent these negative effects, excess cysteine was mainly incorporated into glutathione (GSH), the intracellular level of which increased by 3 times, and was also exported to the medium and partially degraded to form H2S with participation of 3-mercaptopyruvate sulfotransferase (3MST). The addition of Pi to starving cells led to a sharp recovery of respiration and growth, GSH efflux into the medium and K+ influx into the cells. A pronounced coupling of Pi, GSH, and K+ fluxes was shown upon Pi depletion and addition, which may be necessary to maintain the ionic balance in the cytoplasm. We suggest that processes aimed at restoring cysteine homeostasis may be an integral part of the universal response to stress under different types of stress and for different types of bacteria.
Collapse
Affiliation(s)
- Galina V Smirnova
- Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center, Russian Academy of Sciences, ul. Goleva 13, Perm, 614081, Russia.
| | - Aleksey V Tyulenev
- Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center, Russian Academy of Sciences, ul. Goleva 13, Perm, 614081, Russia.
| | - Kseniya V Bezmaternykh
- Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center, Russian Academy of Sciences, ul. Goleva 13, Perm, 614081, Russia.
| | - Nadezda G Muzyka
- Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center, Russian Academy of Sciences, ul. Goleva 13, Perm, 614081, Russia.
| | - Vadim Y Ushakov
- Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center, Russian Academy of Sciences, ul. Goleva 13, Perm, 614081, Russia.
| | - Oleg N Oktyabrsky
- Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center, Russian Academy of Sciences, ul. Goleva 13, Perm, 614081, Russia.
| |
Collapse
|
30
|
North H, McLaughlin M, Fiebig A, Crosson S. The Caulobacter NtrB-NtrC two-component system bridges nitrogen assimilation and cell development. J Bacteriol 2023; 205:e0018123. [PMID: 37791753 PMCID: PMC10601693 DOI: 10.1128/jb.00181-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 09/03/2023] [Indexed: 10/05/2023] Open
Abstract
A suite of molecular sensory systems enables Caulobacter to control growth, development, and reproduction in response to levels of essential elements. The bacterial enhancer-binding protein (bEBP) NtrC and its cognate sensor histidine kinase, NtrB, are key regulators of nitrogen assimilation in many bacteria, but their roles in Caulobacter metabolism and development are not well defined. Notably, Caulobacter NtrC is an unconventional bEBP that lacks the σ54-interacting loop commonly known as the GAFTGA motif. Here we show that deletion of Caulobacter crescentus ntrC slows cell growth in complex medium and that ntrB and ntrC are essential when ammonium is the sole nitrogen source due to their requirement for glutamine synthetase expression. Random transposition of a conserved IS3-family mobile genetic element frequently rescued the growth defect of ntrC mutant strains by restoring transcription of the glnBA operon, revealing a possible role for IS3 transposition in shaping the evolution of Caulobacter populations during nutrient limitation. We further identified dozens of direct NtrC-binding sites on the C. crescentus chromosome, with a large fraction located near genes involved in polysaccharide biosynthesis. The majority of binding sites align with those of the essential nucleoid-associated protein, GapR, or the cell cycle regulator, MucR1. NtrC is therefore predicted to directly impact the regulation of cell cycle and cell development. Indeed, loss of NtrC function led to elongated polar stalks and elevated synthesis of cell envelope polysaccharides. This study establishes regulatory connections between NtrC, nitrogen metabolism, polar morphogenesis, and envelope polysaccharide synthesis in Caulobacter. IMPORTANCE Bacteria balance cellular processes with the availability of nutrients in their environment. The NtrB-NtrC two-component signaling system is responsible for controlling nitrogen assimilation in many bacteria. We have characterized the effect of ntrB and ntrC deletion on Caulobacter growth and development and uncovered a role for spontaneous IS element transposition in the rescue of transcriptional and nutritional deficiencies caused by ntrC mutation. We further defined the regulon of Caulobacter NtrC, a bacterial enhancer-binding protein, and demonstrate that it shares specific binding sites with essential proteins involved in cell cycle regulation and chromosome organization. Our work provides a comprehensive view of transcriptional regulation mediated by a distinctive NtrC protein, establishing its connection to nitrogen assimilation and developmental processes in Caulobacter.
Collapse
Affiliation(s)
- Hunter North
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Maeve McLaughlin
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Aretha Fiebig
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Sean Crosson
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| |
Collapse
|
31
|
Li H, Bhattarai B, Barber M, Goel R. Stringent Response of Cyanobacteria and Other Bacterioplankton during Different Stages of a Harmful Cyanobacterial Bloom. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:16016-16032. [PMID: 37819800 DOI: 10.1021/acs.est.3c03114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
We conducted a field study to investigate the role of stringent response in cyanobacteria and coexisting bacterioplankton during nutrient-deprived periods at various stages of bloom in a freshwater lake (Utah Lake) for the first time. Using metagenomics and metatranscriptomics analyses, we examined the cyanobacterial ecology and expression of important functional genes related to stringent response, N and P metabolism, and regulation. Our findings mark a significant advancement in understanding the mechanisms by which toxic cyanobacteria survive and proliferate during nitrogen (N) and phosphorus (P) limitations. We successfully identified and analyzed the metagenome-assembled genomes (MAGs) of the dominant bloom-forming cyanobacteria, namely, Dolichospermum circinale, Aphanizomenon flos-aquae UKL13-PB, Planktothrix agardhii, and Microcystis aeruginosa. By mapping RNA-seq data to the coding sequences of the MAGs, we observed that these four prevalent cyanobacteria species activated multiple functions to adapt to the depletion of inorganic nutrients. During and after the blooms, the four dominant cyanobacteria species expressed high levels of transcripts related to toxin production, such as microcystins (mcy), anatoxins (ana), and cylindrospermopsins (cyr). Additionally, genes associated with polyphosphate (poly-P) storage and the stringent response alarmone (p)ppGpp synthesis/hydrolysis, including ppk, relA, and spoT, were highly activated in both cyanobacteria and bacterioplankton. Under N deficiency, the main N pathways shifted from denitrification and dissimilatory nitrate reduction in bacterioplankton toward N2-fixing and assimilatory nitrate reduction in certain cyanobacteria with a corresponding shift in the community composition. P deprivation triggered a stringent response mediated by spoT-dependent (p)ppGpp accumulation and activation of the Pho regulon in both cyanobacteria and bacterioplankton, facilitating inorganic and organic P uptake. The dominant cyanobacterial MAGs exhibited the presence of multiple alkaline phosphatase (APase) transcripts (e.g., phoA in Dolichospermum, phoX in Planktothrix, and Microcystis), suggesting their ability to synthesize and release APase enzymes to convert ambient organic P into bioavailable forms. Conversely, transcripts associated with bacterioplankton-dominated pathways like denitrification were low and did not align with the occurrence of intense cyanoHABs. The strong correlations observed among N, P, stringent response metabolisms and the succession of blooms caused by dominant cyanobacterial species provide evidence that the stringent response, induced by nutrient limitation, may activate unique N and P functions in toxin-producing cyanobacteria, thereby sustaining cyanoHABs.
Collapse
Affiliation(s)
- Hanyan Li
- Institute for Environmental Genomics, The University of Oklahoma, 101 David L Boren Blvd, Norman, Oklahoma 73019, United States
| | - Bishav Bhattarai
- Department of Civil and Environmental Engineering, The University of Utah, 110 S Central Campus, Salt Lake City, Utah 84112, United States
| | - Michael Barber
- Department of Civil and Environmental Engineering, The University of Utah, 110 S Central Campus, Salt Lake City, Utah 84112, United States
| | - Ramesh Goel
- Department of Civil and Environmental Engineering, The University of Utah, 110 S Central Campus, Salt Lake City, Utah 84112, United States
| |
Collapse
|
32
|
Barra PJ, Duran P, Delgado M, Viscardi S, Claverol S, Larama G, Dumont M, Mora MDLL. Proteomic response to phosphorus deficiency and aluminum stress of three aluminum-tolerant phosphobacteria isolated from acidic soils. iScience 2023; 26:107910. [PMID: 37790272 PMCID: PMC10543181 DOI: 10.1016/j.isci.2023.107910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 07/27/2023] [Accepted: 09/11/2023] [Indexed: 10/05/2023] Open
Abstract
Aluminum (Al)-tolerant phosphobacteria enhance plant growth in acidic soils by improving Al complexing and phosphorus (P) availability. However, the impact of Al stress and P deficiency on bacterial biochemistry and physiology remains unclear. We investigated the single and mutual effects of Al stress (10 mM) and P deficiency (0.05 mM) on the proteome of three aluminum-tolerant phosphobacteria: Enterobacter sp. 198, Enterobacter sp. RJAL6, and Klebsiella sp. RCJ4. Cultivated under varying conditions, P deficiency upregulated P metabolism proteins while Al exposure downregulated iron-sulfur and heme-containing proteins and upregulated iron acquisition proteins. This demonstrated that Al influence on iron homeostasis and bacterial central metabolism. This study offers crucial insights into bacterial behavior in acidic soils, benefiting the development of bioinoculants for crops facing Al toxicity and P deficiency. This investigation marks the first proteomic study on the interaction between high Al and P deficiency in acid soils-adapted bacteria.
Collapse
Affiliation(s)
- Patricio Javier Barra
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile
- Biocontrol Research Laboratory, Universidad de La Frontera, Temuco 4811230, Chile
| | - Paola Duran
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile
- Biocontrol Research Laboratory, Universidad de La Frontera, Temuco 4811230, Chile
- Facultad de Ciencias Agropecuarias y Medioambiente, Departamento de Producción Agropecuaria, Universidad de La Frontera, Temuco 4811230, Chile
| | - Mabel Delgado
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile
| | - Sharon Viscardi
- Escuela de la Salud, Campus San Francisco, Universidad Católica de Temuco, Temuco 4811230, Chile
| | - Stéphane Claverol
- Plateforme Protéome, Centre Génomique Fonctionnelle de Bordeaux, Université de Bordeaux, Bordeaux, France
| | - Giovanni Larama
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile
- Biocontrol Research Laboratory, Universidad de La Frontera, Temuco 4811230, Chile
| | - Marc Dumont
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - María de la Luz Mora
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile
| |
Collapse
|
33
|
Garaycochea S, Altier NA, Leoni C, Neal AL, Romero H. Abundance and phylogenetic distribution of eight key enzymes of the phosphorus biogeochemical cycle in grassland soils. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:352-369. [PMID: 37162018 PMCID: PMC10472533 DOI: 10.1111/1758-2229.13159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 04/12/2023] [Indexed: 05/11/2023]
Abstract
Grassland biomes provide valuable ecosystem services, including nutrient cycling. Organic phosphorus (Po) represents more than half of the total P in soils. Soil microorganisms release organic P through enzymatic processes, with alkaline phosphatases, acid phosphatases and phytases being the key P enzymes involved in the cycling of organic P. This study analysed 74 soil metagenomes from 17 different grassland biomes worldwide to evaluate the distribution and abundance of eight key P enzymes (PhoD, PhoX, PhoA, Nsap-A, Nsap-B, Nsap-C, BPP and CPhy) and their relationship with environmental factors. Our analyses showed that alkaline phosphatase phoD was the dataset's most abundant P-enzyme encoding genes, with a wide phylogenetic distribution. Followed by the acid phosphatases Nsap-A and Nsap-C showed similar abundance but a different distribution in their respective phylogenetic trees. Multivariate analyses revealed that pH, Tmax , SOC and soil moisture were associated with the abundance and diversity of all genes studied. PhoD and phoX genes strongly correlated with SOC and clay, and the phoX gene was more common in soils with low to medium SOC and neutral pH. In particular, P-enzyme genes tended to respond in a positively correlated manner among them, suggesting a complex relationship of abundance and diversity among them.
Collapse
Affiliation(s)
- Silvia Garaycochea
- Instituto Nacional de Investigación Agropecuaria (INIA)Estación Experimental INIA Las BrujasCanelonesUruguay
| | - Nora Adriana Altier
- Instituto Nacional de Investigación Agropecuaria (INIA)Estación Experimental INIA Las BrujasCanelonesUruguay
| | - Carolina Leoni
- Instituto Nacional de Investigación Agropecuaria (INIA)Estación Experimental INIA Las BrujasCanelonesUruguay
| | - Andrew L. Neal
- Net‐Zero and Resilient FarmingRothamsted Research, North WykeOkehamptonUK
| | - Héctor Romero
- Laboratorio de Organización y Evolución del Genoma/Genómica Evolutiva, Departamento de Ecología y Evolución, Facultad de Ciencias/CUREUniversidad de la RepúblicaMaldonadoUruguay
| |
Collapse
|
34
|
Mujakić I, Cabello-Yeves PJ, Villena-Alemany C, Piwosz K, Rodriguez-Valera F, Picazo A, Camacho A, Koblížek M. Multi-environment ecogenomics analysis of the cosmopolitan phylum Gemmatimonadota. Microbiol Spectr 2023; 11:e0111223. [PMID: 37732776 PMCID: PMC10581226 DOI: 10.1128/spectrum.01112-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 08/02/2023] [Indexed: 09/22/2023] Open
Abstract
Gemmatimonadota is a diverse bacterial phylum commonly found in environments such as soils, rhizospheres, fresh waters, and sediments. So far, the phylum contains just six cultured species (five of them sequenced), which limits our understanding of their diversity and metabolism. Therefore, we analyzed over 400 metagenome-assembled genomes (MAGs) and 5 culture-derived genomes representing Gemmatimonadota from various aquatic environments, hydrothermal vents, sediments, soils, and host-associated (with marine sponges and coral) species. The principal coordinate analysis based on the presence/absence of genes in Gemmatimonadota genomes and phylogenomic analysis documented that marine and host-associated Gemmatimonadota were the most distant from freshwater and wastewater species. A smaller genome size and coding sequences (CDS) number reduction were observed in marine MAGs, pointing to an oligotrophic environmental adaptation. Several metabolic pathways are restricted to specific environments. For example, genes for anoxygenic phototrophy were found only in freshwater, wastewater, and soda lake sediment genomes. There were several genomes from soda lake sediments and wastewater containing type IC/ID ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). Various genomes from wastewater harbored bacterial type II RuBisCO, whereas RuBisCO-like protein was found in genomes from fresh waters, soil, host-associated, and marine sediments. Gemmatimonadota does not contain nitrogen fixation genes; however, the nosZ gene, involved in the reduction of N2O, was present in genomes from most environments, missing only in marine water and host-associated Gemmatimonadota. The presented data suggest that Gemmatimonadota evolved as an organotrophic species relying on aerobic respiration and then remodeled its genome inventory when adapting to particular environments. IMPORTANCE Gemmatimonadota is a rarely studied bacterial phylum consisting of a handful of cultured species. Recent culture-independent studies documented that these organisms are distributed in many environments, including soil, marine, fresh, and waste waters. However, due to the lack of cultured species, information about their metabolic potential and environmental role is scarce. Therefore, we collected Gemmatimonadota metagenome-assembled genomes (MAGs) from different habitats and performed a systematic analysis of their genomic characteristics and metabolic potential. Our results show how Gemmatimonadota have adapted their genomes to different environments.
Collapse
Affiliation(s)
- Izabela Mujakić
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Pedro J. Cabello-Yeves
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Paterna, Valencia, Spain
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Cristian Villena-Alemany
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Kasia Piwosz
- Department of Fisheries Oceanography and Marine Ecology, National Marine Fisheries Research Institute, Gdynia, Poland
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Antonio Picazo
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Paterna, Valencia, Spain
| | - Antonio Camacho
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Paterna, Valencia, Spain
| | - Michal Koblížek
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| |
Collapse
|
35
|
Li J, Yang C, Jousset A, Yang K, Wang X, Xu Z, Yang T, Mei X, Zhong Z, Xu Y, Shen Q, Friman VP, Wei Z. Engineering multifunctional rhizosphere probiotics using consortia of Bacillus amyloliquefaciens transposon insertion mutants. eLife 2023; 12:e90726. [PMID: 37706503 PMCID: PMC10519709 DOI: 10.7554/elife.90726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 09/13/2023] [Indexed: 09/15/2023] Open
Abstract
While bacterial diversity is beneficial for the functioning of rhizosphere microbiomes, multi-species bioinoculants often fail to promote plant growth. One potential reason for this is that competition between different species of inoculated consortia members creates conflicts for their survival and functioning. To circumvent this, we used transposon insertion mutagenesis to increase the functional diversity within Bacillus amyloliquefaciens bacterial species and tested if we could improve plant growth promotion by assembling consortia of highly clonal but phenotypically dissimilar mutants. While most insertion mutations were harmful, some significantly improved B. amyloliquefaciens plant growth promotion traits relative to the wild-type strain. Eight phenotypically distinct mutants were selected to test if their functioning could be improved by applying them as multifunctional consortia. We found that B. amyloliquefaciens consortium richness correlated positively with plant root colonization and protection from Ralstonia solanacearum phytopathogenic bacterium. Crucially, 8-mutant consortium consisting of phenotypically dissimilar mutants performed better than randomly assembled 8-mutant consortia, suggesting that improvements were likely driven by consortia multifunctionality instead of consortia richness. Together, our results suggest that increasing intra-species phenotypic diversity could be an effective way to improve probiotic consortium functioning and plant growth promotion in agricultural systems.
Collapse
Affiliation(s)
- Jingxuan Li
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Chunlan Yang
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Alexandre Jousset
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Keming Yang
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Xiaofang Wang
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Zhihui Xu
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Tianjie Yang
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Xinlan Mei
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Zengtao Zhong
- College of Life Science, Nanjing Agricultural UniversityNanjingChina
| | - Yangchun Xu
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Qirong Shen
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Ville-Petri Friman
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
- Department of Microbiology, University of HelsinkiHelsinkiFinland
| | - Zhong Wei
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| |
Collapse
|
36
|
North H, McLaughlin M, Fiebig A, Crosson S. The Caulobacter NtrB-NtrC two-component system bridges nitrogen assimilation and cell development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.06.543975. [PMID: 37333394 PMCID: PMC10274813 DOI: 10.1101/2023.06.06.543975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
A suite of molecular sensory systems enables Caulobacter to control growth, development, and reproduction in response to levels of essential elements. The bacterial enhancer binding protein (bEBP) NtrC, and its cognate sensor histidine kinase NtrB, are key regulators of nitrogen assimilation in many bacteria, but their roles in Caulobacter metabolism and development are not well defined. Notably, Caulobacter NtrC is an unconventional bEBP that lacks the σ54-interacting loop commonly known as the GAFTGA motif. Here we show that deletion of C. crescentus ntrC slows cell growth in complex medium, and that ntrB and ntrC are essential when ammonium is the sole nitrogen source due to their requirement for glutamine synthetase (glnA) expression. Random transposition of a conserved IS3-family mobile genetic element frequently rescued the growth defect of ntrC mutant strains by restoring transcription of the glnBA operon, revealing a possible role for IS3 transposition in shaping the evolution of Caulobacter populations during nutrient limitation. We further identified dozens of direct NtrC binding sites on the C. crescentus chromosome, with a large fraction located near genes involved in polysaccharide biosynthesis. The majority of binding sites align with those of the essential nucleoid associated protein, GapR, or the cell cycle regulator, MucR1. NtrC is therefore predicted to directly impact the regulation of cell cycle and cell development. Indeed, loss of NtrC function led to elongated polar stalks and elevated synthesis of cell envelope polysaccharides. This study establishes regulatory connections between NtrC, nitrogen metabolism, polar morphogenesis, and envelope polysaccharide synthesis in Caulobacter .
Collapse
Affiliation(s)
- Hunter North
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan USA
| | - Maeve McLaughlin
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan USA
| | - Aretha Fiebig
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan USA
| | - Sean Crosson
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan USA
| |
Collapse
|
37
|
Gorski L, Noriega AA. Comparison of Phenotype Nutritional Profiles and Phosphate Metabolism Genes in Four Serovars of Salmonella enterica from Water Sources. Microorganisms 2023; 11:2109. [PMID: 37630669 PMCID: PMC10459026 DOI: 10.3390/microorganisms11082109] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/03/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
The surveillance of foods for Salmonella is hindered by bias in common enrichment media where serovars implicated in human illness are outgrown by less virulent serovars. We examined four Salmonella serovars, two common in human illness (Enteritidis and Typhimurium) and two that often dominate enrichments (Give and Kentucky), for factors that might influence culture bias. The four serovars had similar growth kinetics in Tryptic Soy Broth and Buffered Peptone Water. Phenotype microarray analysis with 950 chemical substrates to assess nutrient utilization and stress resistance revealed phenotype differences between serovars. Strains of S. Enteritidis had better utilization of plant-derived sugars such as xylose, mannitol, rhamnose, and fructose, while S. Typhimurium strains were able to metabolize tagatose. Strains of S. Kentucky used more compounds as phosphorus sources and grew better with inorganic phosphate as the sole phosphorus source. The sequences of nine genes involved in phosphate metabolism were compared, and there were differences between serovars in the catalytic ATP-binding domain of the histidine kinase phoR. Analysis of the predicted PhoR amino acid sequences from additional Salmonella genomes indicated a conservation of sequences each within the Typhimurium, Give, and Enteritidis serovars. However, three different PhoR versions were observed in S. Kentucky.
Collapse
Affiliation(s)
- Lisa Gorski
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, United States Department of Agriculture, Albany, CA 94710, USA
| | | |
Collapse
|
38
|
Ferrarezi JA, Defant H, de Souza LF, Azevedo JL, Hungria M, Quecine MC. Meta-omics integration approach reveals the effect of soil native microbiome diversity in the performance of inoculant Azospirillum brasilense. FRONTIERS IN PLANT SCIENCE 2023; 14:1172839. [PMID: 37457347 PMCID: PMC10340089 DOI: 10.3389/fpls.2023.1172839] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/19/2023] [Indexed: 07/18/2023]
Abstract
Plant growth promoting bacteria (PGPB) have been used as integrative inputs to minimize the use of chemical fertilizers. However, a holistic comprehension about PGPB-plant-microbiome interactions is still incipient. Furthermore, the interaction among PGPB and the holobiont (host-microbiome association) represent a new frontier to plant breeding programs. We aimed to characterize maize bulk soil and rhizosphere microbiomes in irradiated soil (IS) and a native soil (NS) microbial community gradient (dilution-to-extinction) with Azospirillum brasilense Ab-V5, a PGPB commercial inoculant. Our hypothesis was that plant growth promotion efficiency is a result of PGPB niche occupation and persistence according to the holobiont conditions. The effects of Ab-V5 and NS microbial communities were evaluated in microcosms by a combined approach of microbiomics (species-specific qPCR, 16S rRNA metataxonomics and metagenomics) and plant phenomics (conventional and high-throughput methods). Our results revealed a weak maize growth promoting effect of Ab-V5 inoculation in undiluted NS, contrasting the positive effects of NS dilutions 10-3, 10-6, 10-9 and IS with Ab-V5. Alpha diversity in NS + Ab-V5 soil samples was higher than in all other treatments in a time course of 25 days after sowing (DAS). At 15 DAS, alpha diversity indexes were different between NS and IS, but similar in all NS dilutions in rhizospheric samples. These differences were not persistent at 25 DAS, demonstrating a stabilization process in the rhizobiomes. In NS 10-3 +Ab-V5 and NS 10-6 Ab-V5, Ab-V5 persisted in the maize rhizosphere until 15 DAS in higher abundances compared to NS. In NS + Ab-V5, abundance of six taxa were positively correlated with response to (a)biotic stresses in plant-soil interface. Genes involved in bacterial metabolism of riboses and amino acids, and cresol degradation were abundant on NS 10-3 + Ab-V5, indicating that these pathways can contribute to plant growth promotion and might be a result of Ab-V5 performance as a microbial recruiter of beneficial functions to the plant. Our results demonstrated the effects of holobiont on Ab-V5 performance. The meta-omics integration supported by plant phenomics opens new perspectives to better understanding of inoculants-holobiont interaction and for developing better strategies for optimization in the use of microbial products.
Collapse
Affiliation(s)
- Jessica Aparecida Ferrarezi
- Laboratory of Genetics of Microorganisms “Prof. Joao Lucio de Azevedo”, Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Heloísa Defant
- Laboratory of Genetics of Microorganisms “Prof. Joao Lucio de Azevedo”, Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Leandro Fonseca de Souza
- Laboratory of Genetics of Microorganisms “Prof. Joao Lucio de Azevedo”, Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - João Lúcio Azevedo
- Laboratory of Genetics of Microorganisms “Prof. Joao Lucio de Azevedo”, Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | | | - Maria Carolina Quecine
- Laboratory of Genetics of Microorganisms “Prof. Joao Lucio de Azevedo”, Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| |
Collapse
|
39
|
Cruz-Bautista R, Ruíz-Villafán B, Romero-Rodríguez A, Rodríguez-Sanoja R, Sánchez S. Trends in the two-component system's role in the synthesis of antibiotics by Streptomyces. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12623-z. [PMID: 37341754 DOI: 10.1007/s00253-023-12623-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/30/2023] [Accepted: 06/05/2023] [Indexed: 06/22/2023]
Abstract
Despite the advances in understanding the regulatory networks for secondary metabolite production in Streptomyces, the participation of the two-component systems (TCS) in this process still requires better characterization. These sensing systems and their responses to environmental stimuli have been described by evaluating mutant strains with techniques that allow in-depth regulatory responses. However, defining the stimulus that triggers their activation is still a task. The transmembrane nature of the sensor kinases and the high content of GC in the streptomycetes represent significant challenges in their study. In some examples, adding elements to the assay medium has determined the respective ligand. However, a complete TCS description and characterization requires specific amounts of the involved proteins that are most difficult to obtain. The availability of enough sensor histidine kinase concentrations could facilitate the identification of the ligand-protein interaction, and besides would allow the establishment of its phosphorylation mechanisms and determine their tridimensional structure. Similarly, the advances in the development of bioinformatics tools and novel experimental techniques also promise to accelerate the TCSs description and provide knowledge on their participation in the regulation processes of secondary metabolite formation. This review aims to summarize the recent advances in the study of TCSs involved in antibiotic biosynthesis and to discuss alternatives to continue their characterization. KEY POINTS: • TCSs are the environmental signal transducers more abundant in nature. • The Streptomyces have some of the highest number of TCSs found in bacteria. • The study of signal transduction between SHKs and RRs domains is a big challenge.
Collapse
Affiliation(s)
- Rodrigo Cruz-Bautista
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CdMx, 04510, Mexico City, Mexico.
| | - Beatriz Ruíz-Villafán
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CdMx, 04510, Mexico City, Mexico
| | - Alba Romero-Rodríguez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CdMx, 04510, Mexico City, Mexico
| | - Romina Rodríguez-Sanoja
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CdMx, 04510, Mexico City, Mexico
| | - Sergio Sánchez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CdMx, 04510, Mexico City, Mexico.
| |
Collapse
|
40
|
Keroack CD, Elsworth B, Tennessen JA, Paul AS, Hua R, Ramirez-Ramirez L, Ye S, Moreira CM, Meyers MJ, Zarringhalam K, Duraisingh MT. Comparative chemical genomics in Babesia species identifies the alkaline phosphatase phoD as a novel determinant of resistance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.13.544849. [PMID: 37398106 PMCID: PMC10312741 DOI: 10.1101/2023.06.13.544849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Babesiosis is an emerging zoonosis and widely distributed veterinary infection caused by 100+ species of Babesia parasites. The diversity of Babesia parasites, coupled with the lack of potent inhibitors necessitates the discovery of novel conserved druggable targets for the generation of broadly effective antibabesials. Here, we describe a comparative chemogenomics (CCG) pipeline for the identification of novel and conserved targets. CCG relies on parallel in vitro evolution of resistance in independent populations of evolutionarily-related Babesia spp. ( B. bovis and B. divergens ). We identified a potent antibabesial inhibitor from the Malaria Box, MMV019266. We were able to select for resistance to this compound in two species of Babesia, achieving 10-fold or greater resistance after ten weeks of intermittent selection. After sequencing of multiple independently derived lines in the two species, we identified mutations in a single conserved gene in both species: a membrane-bound metallodependent phosphatase (putatively named PhoD). In both species, the mutations were found in the phoD-like phosphatase domain, proximal to the predicted ligand binding site. Using reverse genetics, we validated that mutations in PhoD confer resistance to MMV019266. We have also demonstrated that PhoD localizes to the endomembrane system and partially with the apicoplast. Finally, conditional knockdown and constitutive overexpression of PhoD alter the sensitivity to MMV019266 in the parasite: overexpression of PhoD results in increased sensitivity to the compound, while knockdown increases resistance, suggesting PhoD is a resistance mechanism. Together, we have generated a robust pipeline for identification of resistance loci, and identified PhoD as a novel determinant of resistance in Babesia species. Highlights Use of two species for in vitro evolution identifies a high confidence locus associated with resistance Resistance mutation in phoD was validated using reverse genetics in B. divergens Perturbation of phoD using function genetics results in changes in the level of resistance to MMV019266Epitope tagging reveals localization to the ER/apicoplast, a conserved localization with a similar protein in diatoms Together, phoD is a novel resistance determinant in multiple Babesia spp .
Collapse
|
41
|
Sattrapai N, Chaiprom U, Lindow SE, Chatnaparat T. A Phosphate Uptake System Is Required for Xanthomonas citri pv. glycines Virulence in Soybean. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:261-272. [PMID: 36574016 DOI: 10.1094/mpmi-11-22-0241-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The genes encoding the phosphate uptake system in Xanthomonas citri pv. glycines 12-2 were previously found to be upregulated when in soybean leaves. This study thus explored the role of the phosphate uptake system on its virulence to soybean. While phoB and pstSCAB mutants were greatly impaired in both inciting disease symptoms and growth in soybean, the virulence and growth in soybean of a phoU mutant was not reduced when compared with the wild-type strain. The expression of phoB and pstSCAB was highly induced in phosphate-deficient media. In addition, the expression of phoB, assessed with a fusion to a promoterless ice nucleation reporter gene, was greatly increased in soybean leaves, confirming that the soybean apoplast is a phosphorus-limited habitat for X. citri pv. glycines. Global gene expression profiles of phoB and phoU mutants of X. citri pv. glycines conducted under phosphate-limitation conditions in vitro, using RNA-seq, revealed that PhoB positively regulated genes involved in signal transduction, the xcs cluster type II secretion system, cell motility, and chemotaxis, while negatively regulating cell wall and membrane biogenesis, DNA replication and recombination and repair, and several genes with unknown function. PhoU also positively regulated the same genes involved in cell motility and chemotaxis. The severity of bacterial pustule disease was decreased in soybean plants grown under high phosphate fertilization conditions, demonstrating that high phosphate availability in soybean plants can affect infection by X. citri pv. glycines by modulation of the expression of phosphate uptake systems. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
Collapse
Affiliation(s)
- Nutthakan Sattrapai
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok, Thailand
- Center for Advanced Studies for Agriculture and Food (CASAF), Kasetsart University, Bangkok, Thailand
| | - Usawadee Chaiprom
- National Biobank of Thailand (NBT), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Steven E Lindow
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, U.S.A
| | - Tiyakhon Chatnaparat
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok, Thailand
- Center for Advanced Studies for Agriculture and Food (CASAF), Kasetsart University, Bangkok, Thailand
| |
Collapse
|
42
|
Shah BS, Ford BA, Varkey D, Mikolajek H, Orr C, Mykhaylyk V, Owens RJ, Paulsen IT. Marine picocyanobacterial PhnD1 shows specificity for various phosphorus sources but likely represents a constitutive inorganic phosphate transporter. THE ISME JOURNAL 2023:10.1038/s41396-023-01417-w. [PMID: 37087502 DOI: 10.1038/s41396-023-01417-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 03/14/2023] [Accepted: 04/13/2023] [Indexed: 04/24/2023]
Abstract
Despite being fundamental to multiple biological processes, phosphorus (P) availability in marine environments is often growth-limiting, with generally low surface concentrations. Picocyanobacteria strains encode a putative ABC-type phosphite/phosphate/phosphonate transporter, phnDCE, thought to provide access to an alternative phosphorus pool. This, however, is paradoxical given most picocyanobacterial strains lack known phosphite degradation or carbon-phosphate lyase pathway to utilise alternate phosphorus pools. To understand the function of the PhnDCE transport system and its ecological consequences, we characterised the PhnD1 binding proteins from four distinct marine Synechococcus isolates (CC9311, CC9605, MITS9220, and WH8102). We show the Synechococcus PhnD1 proteins selectively bind phosphorus compounds with a stronger affinity for phosphite than for phosphate or methyl phosphonate. However, based on our comprehensive ligand screening and growth experiments showing Synechococcus strains WH8102 and MITS9220 cannot utilise phosphite or methylphosphonate as a sole phosphorus source, we hypothesise that the picocyanobacterial PhnDCE transporter is a constitutively expressed, medium-affinity phosphate transporter, and the measured affinity of PhnD1 to phosphite or methyl phosphonate is fortuitous. Our MITS9220_PhnD1 structure explains the comparatively lower affinity of picocyanobacterial PhnD1 for phosphate, resulting from a more limited H-bond network. We propose two possible physiological roles for PhnD1. First, it could function in phospholipid recycling, working together with the predicted phospholipase, TesA, and alkaline phosphatase. Second, by having multiple transporters for P (PhnDCE and Pst), picocyanobacteria could balance the need for rapid transport during transient episodes of higher P availability in the environment, with the need for efficient P utilisation in typical phosphate-deplete conditions.
Collapse
Affiliation(s)
- Bhumika S Shah
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia.
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia.
| | - Benjamin A Ford
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
| | - Deepa Varkey
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
| | - Halina Mikolajek
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
| | - Christian Orr
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
| | - Vitaliy Mykhaylyk
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
| | - Raymond J Owens
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Structural Biology, Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot, UK
| | - Ian T Paulsen
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia.
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia.
| |
Collapse
|
43
|
Yu Z, Li W, Ge C, Sun X, Wang J, Shen X, Yuan Q. Functional expansion of the natural inorganic phosphorus starvation response system in Escherichia coli. Biotechnol Adv 2023; 66:108154. [PMID: 37062526 DOI: 10.1016/j.biotechadv.2023.108154] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 04/08/2023] [Accepted: 04/09/2023] [Indexed: 04/18/2023]
Abstract
Phosphorus, an indispensable nutrient, plays an essential role in cell composition, metabolism, and signal transduction. When inorganic phosphorus (Pi) is scarce, the Pi starvation response in E. coli is activated to increase phosphorus acquisition and drive the cells into a non-growing state to reduce phosphorus consumption. In the six decades of research history, the initiation, output, and shutdown processes of the Pi starvation response have been extensively studied. Simultaneously, Pi starvation has been used in biosensor development, recombinant protein production, and natural product biosynthesis. In this review, we focus on the output process and the applications of the Pi starvation response that have not been summarized before. Meanwhile, based on the current status of mechanistic studies and applications, we propose practical strategies to develop the natural Pi starvation response into a multifunctional and standardized regulatory system in four aspects, including response threshold, temporal expression, intensity range, and bifunctional regulation, which will contribute to its broader application in more fields such as industrial production, medical analysis, and environmental protection.
Collapse
Affiliation(s)
- Zheng Yu
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Wenna Li
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Chang Ge
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xinxiao Sun
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jia Wang
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xiaolin Shen
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Qipeng Yuan
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
| |
Collapse
|
44
|
Nishiyama T, Hoshino R, Ueda K. Characterization of 5'-nucleotidases secreted from Streptomyces. Appl Microbiol Biotechnol 2023; 107:2289-2302. [PMID: 36820897 DOI: 10.1007/s00253-023-12426-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/26/2023] [Accepted: 02/01/2023] [Indexed: 02/24/2023]
Abstract
To study the ability of Streptomyces to utilize environmental nucleotides, we screened for strains exhibiting extracellular 5'-inosine monophosphate (IMP)-dephosphorylating activity in our collection of soil isolates and obtained two producers: NE5-10 and Y2F8-2. The enzyme responsible for the activity was purified from the culture supernatant of each strain, and its mass spectral data were used to identify the coding sequence. The gene was successfully identified in the whole genome sequence of each strain; it was located in a conserved gene cluster of phosphate-related functions and encoded an approximately 600-amino acid long protein containing an N-terminal secretion signal. The mature part of the protein exhibited similarity to a known bacterial 5'-nucleotidase. The locus of the 5'-nucleotidase gene contained genes encoding proteins involved in phosphate utilization. The conserved gene arrangement of the locus in various Streptomyces genomes suggested the genetic region to be involved in phosphate-scavenging in this group of bacteria. Phylogenetic analysis demonstrated that the isolated Streptomyces enzymes represent an uncharacterized group of bacterial 5'-nucleotidases. Enzymatic characterization of the two Streptomyces enzymes demonstrated that both enzymes exhibited 5'-nucleotidase activity but differed in terms of optimal temperature and pH, dependence on divalent cations, and substrate specificity. The Km and Vmax values of the 5'-IMP-dephosphorylating activity were 0.239 mM and 9.47 U/mg, respectively, for NE5-10 and 0.221 mM and 38.17 U/mg, respectively, for Y2F8-2. Enzyme activity in the culture broth of the two Streptomyces producers occurred in a phosphate-limitation-dependent manner, supporting their involvement in the acquisition of phosphorus. KEY POINTS: • We purified and characterized nucleotidases from two Streptomyces. • Two nucleotidases were presumed to be involved in phosphate acquisition. • It showed diversity in phosphate acquisition among microorganisms.
Collapse
Affiliation(s)
- Tatsuya Nishiyama
- Life Science Research Center, College of Bioresource Sciences, Nihon University, 1866 Kameino, 252-0880, Fujisawa, Japan.
| | - Rio Hoshino
- Life Science Research Center, College of Bioresource Sciences, Nihon University, 1866 Kameino, 252-0880, Fujisawa, Japan
| | - Kenji Ueda
- Life Science Research Center, College of Bioresource Sciences, Nihon University, 1866 Kameino, 252-0880, Fujisawa, Japan
| |
Collapse
|
45
|
Wachter S, Larson CL, Virtaneva K, Kanakabandi K, Darwitz B, Crews B, Storrud K, Heinzen RA, Beare PA. A Survey of Two-Component Systems in Coxiella burnetii Reveals Redundant Regulatory Schemes and a Requirement for an Atypical PhoBR System in Mammalian Cell Infection. J Bacteriol 2023; 205:e0041622. [PMID: 36847507 PMCID: PMC10029714 DOI: 10.1128/jb.00416-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 12/20/2022] [Indexed: 03/01/2023] Open
Abstract
Coxiella burnetii is an obligate intracellular bacterium and the etiological agent of Q fever in humans. C. burnetii transitions between a replicative, metabolically active large-cell variant (LCV) and a spore-like, quiescent small-cell variant (SCV) as a likely mechanism to ensure survival between host cells and mammalian hosts. C. burnetii encodes three canonical two-component systems, four orphan hybrid histidine kinases, five orphan response regulators, and a histidine phosphotransfer protein, which have been speculated to play roles in the signaling required for C. burnetii morphogenesis and virulence. However, very few of these systems have been characterized. By employing a CRISPR interference system for genetic manipulation of C. burnetii, we created single- and multigene transcriptional knockdown strains targeting most of these signaling genes. Through this, we revealed a role for the C. burnetii PhoBR canonical two-component system in virulence, regulation of [Pi] maintenance, and Pi transport. We also outline a novel mechanism by which PhoBR function may be regulated by an atypical PhoU-like protein. We also determined that the GacA.2/GacA.3/GacA.4/GacS orphan response regulators coordinately and disparately regulate expression of SCV-associated genes in C. burnetii LCVs. These foundational results will inform future studies on the role of C. burnetii two-component systems in virulence and morphogenesis. IMPORTANCE C. burnetii is an obligate intracellular bacterium with a spore-like stability allowing it to survive long periods of time in the environment. This stability is likely due to its biphasic developmental cycle, whereby it can transition from an environmentally stable small-cell variant (SCV) to a metabolically active large-cell variant (LCV). Here, we define the role of two-component phosphorelay systems (TCS) in C. burnetii's ability to survive within the harsh environment contained in the phagolysosome of host cells. We show that the canonical PhoBR TCS has an important role in C. burnetii virulence and phosphate sensing. Further examination of the regulons controlled by orphan regulators indicated a role in modulating gene expression of SCV-associated genes, including genes essential for cell wall remodeling.
Collapse
Affiliation(s)
- Shaun Wachter
- Coxiella Pathogenesis Section, Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
- Vaccine and Infectious Disease Organization, Saskatoon, Saskatchewan, Canada
| | - Charles L. Larson
- Coxiella Pathogenesis Section, Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Kimmo Virtaneva
- Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, Hamilton, Montana, USA
| | - Kishore Kanakabandi
- Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, Hamilton, Montana, USA
| | - Benjamin Darwitz
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Ben Crews
- Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, Hamilton, Montana, USA
| | - Keelee Storrud
- Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, Hamilton, Montana, USA
| | - Robert A. Heinzen
- Coxiella Pathogenesis Section, Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Paul A. Beare
- Coxiella Pathogenesis Section, Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
- Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, Hamilton, Montana, USA
| |
Collapse
|
46
|
Thomas DR, Newton HJ. Complex Signaling Networks Control Coxiella burnetii. J Bacteriol 2023; 205:e0001323. [PMID: 36847508 PMCID: PMC10029709 DOI: 10.1128/jb.00013-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
A recent study by S. Wachter, C. L. Larson, K. Virtaneva, K. Kanakabandi, et al. (J Bacteriol 205:e00416-22, 2023, https://doi.org/10.1128/JB.00416-22) utilizes new technologies to examine the role of two-component systems in Coxiella burnetii. This research demonstrates that the zoonotic pathogen C. burnetii mediates complex transcriptional control, throughout different bacterial phases and environmental conditions, with relatively few regulatory elements.
Collapse
Affiliation(s)
- David R. Thomas
- Infection Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Hayley J. Newton
- Infection Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| |
Collapse
|
47
|
Fang L, Zheng X, Sun Z, Li Y, Deng J, Zhou YI. Characterization of a Plant Growth-Promoting Endohyphal Bacillus subtilis in Fusarium acuminatum from Spiranthes sinensis. Pol J Microbiol 2023; 72:29-37. [PMID: 36929887 DOI: 10.33073/pjm-2023-007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 02/03/2023] [Indexed: 03/18/2023] Open
Abstract
Successful seed germination and seedling growth in orchids require an association with mycorrhizal fungi. An endophytic Fusarium fungal strain YZU 172038 exhibiting plant growth-promoting (PGP) ability was isolated from the roots of Spiranthes sinensis (Orchidaceae). The harboring endohyphal bacteria were detected in the hypha by SYTO-9 fluorescent nucleic acid staining, fluorescence in situ hybridization (FISH), and PCR amplification of the 16S rDNA gene's region. Consequently, one endohyphal bacterium (EHB) - a strain YZSR384 was isolated and identified as Bacillus subtilis based on morphology, phylogenetic analysis, and genomic information. The results indicated that the strain YZSR384 could significantly promote the growth of rice roots and shoots similar to its host fungus. Its indole acetic acid (IAA) production reached a maximum of 23.361 μg/ml on the sixth day after inoculation. The genome annotation revealed several genes involved in PGP traits, including the clusters of genes encoding the IAA (trpABCDEFS), the siderophores (entABCE), and the dissolving phosphate (pstABCS and phoABDHPR). As an EHB, B. subtilis was first isolated from endophytic Fusarium acuminatum from S. sinensis.
Collapse
Affiliation(s)
- Lan Fang
- 1College of Agriculture, Yangtze University, Jingzhou, China
| | - Xiao Zheng
- 1College of Agriculture, Yangtze University, Jingzhou, China
| | - Zhengxiang Sun
- 1College of Agriculture, Yangtze University, Jingzhou, China
| | - Yanyan Li
- 2Tobacco Research Institute of Hubei Province, Wuhan, China
| | - Jianxin Deng
- 1College of Agriculture, Yangtze University, Jingzhou, China
| | - Y I Zhou
- 1College of Agriculture, Yangtze University, Jingzhou, China
| |
Collapse
|
48
|
Isolation and Genomics of Futiania mangrovii gen. nov., sp. nov., a Rare and Metabolically Versatile Member in the Class Alphaproteobacteria. Microbiol Spectr 2023; 11:e0411022. [PMID: 36541777 PMCID: PMC9927469 DOI: 10.1128/spectrum.04110-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Mangrove microorganisms are a major part of the coastal ecosystem and are directly associated with nutrient cycling. Despite their ecological significance, the collection of culturable mangrove microbes is limited due to difficulties in isolation and cultivation. Here, we report the isolation and genome sequence of strain FT118T, the first cultured representative of a previously uncultivated order UBA8317 within Alphaproteobacteria, based on the combined results of 16S rRNA gene similarity, phylogenomic, and average amino acid identity analyses. We propose Futianiales ord. nov. and Futianiaceae fam. nov. with Futiania as the type genus, and FT118T represents the type species with the name Futiania mangrovii gen. nov, sp. nov. The 16S rRNA gene sequence comparison reveals that this novel order is a rare member but has a ubiquitous distribution across various habitats worldwide, which is corroborated by the experimental confirmation that this isolate can physiologically adapt to a wide range of oxygen levels, temperatures, pH and salinity levels. Biochemical characterization, genomic annotation, and metatranscriptomic analysis of FT118T demonstrate that it is metabolically versatile and active in situ. Genomic analysis reveals adaptive features of Futianiales to fluctuating mangrove environments, including the presence of high- and low-affinity terminal oxidases, N-type ATPase, and the genomic capability of producing various compatible solutes and polyhydroxybutyrate, which possibly allow for the persistence of this novel order across various habitats. Collectively, these results expand the current culture collection of mangrove microorganisms, providing genomic insights of how this novel taxon adapts to fluctuating environments and the culture reference to unravel possible microbe-environment interactions. IMPORTANCE The rare biosphere constitutes an essential part of the microbial community and may drive nutrient cycling and other geochemical processes. However, the difficulty in microbial isolation and cultivation has hampered our understanding of the physiology and ecology of uncultured rare lineages. In this study, we successfully isolated a novel alphaproteobacterium, designated as FT118T, and performed a combination of phenotypic, phylogenetic, and phylogenomic analyses, confirming that this isolate represents the first cultured member of a previously uncultivated order UBA8317 within Alphaproteobacteria. It is a rare species with a ubiquitous distribution across different habitats. Genomic and metatranscriptomic analyses demonstrate that it is metabolically versatile and active in situ, suggesting its potential role in nutrient cycling despite being scarce. This work not only expands the current phylogeny of isolated Alphaproteobacteria but also provides genomic and culture reference to unravel microbial adaptation strategies in mangrove sediments and possible microbe-environment interactions.
Collapse
|
49
|
Differential expression and cross-correlation between global regulator and pho regulon genes involved in decision-making under phosphate stress. J Appl Genet 2023; 64:173-183. [PMID: 36346581 DOI: 10.1007/s13353-022-00735-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 10/10/2022] [Accepted: 10/26/2022] [Indexed: 11/11/2022]
Abstract
The differential gene expression under phosphate stress conditions leads to cross-talk between the global regulator, pho regulon, and metabolic genes. Promoter activity analysis of the selected 23 genes reveals the dynamic nature of real-time gene expression under different phosphate conditions. The expression profiles of the global regulator (rpoD, soxR, soxS, arcB, and fur), pho regulon (phoH, phoR, phoB, and ugpB), and metabolic genes (sdh, pfkA, ldh) varied significantly on phosphate level variation. Under stress conditions, soxR switches expression partners and co-expresses with rpoS instead of soxS. The partner-switching behavior of the genes under a challenging environment represents the intelligence of functional execution and ensures cell survival. The dynamic expression profile of the selected genes applies a time-lagged correlation to provide insight into the differential gene interaction between time-shifted expression profiles. Under different phosphate conditions, the minimum spanning tree graph revealed a different clustering pattern of selected genes depending on the computed distance and its proximity to other promoters.
Collapse
|
50
|
Yin Y, Yang C, Li M, Yang S, Tao X, Zheng Y, Wang X, Chen R. Biochar reduces bioavailability of phosphorus during swine manure composting: Roles of phoD-harboring bacterial community. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 858:159926. [PMID: 36343827 DOI: 10.1016/j.scitotenv.2022.159926] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/25/2022] [Accepted: 10/30/2022] [Indexed: 06/16/2023]
Abstract
The bioavailability of phosphorus is a vital index for evaluating the quality of compost products. This study examined the effects of adding wheat straw biochar (WSB) and bamboo charcoal (BC) on the transformation of various phosphorus fractions during composting, as well as analyzing the roles of the phoD-harboring bacterial community in the transformation of phosphorus fractions. Adding WSB and BC reduced the available phosphorus content in the compost products by 35.2 % and 38.5 %, respectively. Redundancy analysis showed that the alkaline phosphatase content and pH were the most important factors that affected the transformation of phosphorus fractions. The addition of biochar resulted in changes in the composition and structures of the phoD-harboring bacteria communities during composting. In addition, the key bacterial genera that secreted alkaline phosphatase and decomposed different forms of phosphorus under WSB and BC were different compared with those under control. Network and correlation analysis demonstrated that the activities of phoD-harboring bacteria could have been enhanced by biochar to accelerate the consumption of available phosphorus, and the activities of key phosphorus-solubilizing bacteria (Lysobacter, Methylobacterium, and Saccharothrix) might be inhibited when the pH increased, thereby increasing the insoluble phosphorus content.
Collapse
Affiliation(s)
- Yanan Yin
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, No. 13 Yanta Road, Xi'an 710055, PR China; International S&T Cooperation Center for Urban Alternative Water Resources Development, Xi'an University of Architecture and Technology, No. 13 Yanta Road, Xi'an 710055, PR China
| | - Chao Yang
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, No. 13 Yanta Road, Xi'an 710055, PR China
| | - Mengtong Li
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, No. 13 Yanta Road, Xi'an 710055, PR China
| | - Sai Yang
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, No. 13 Yanta Road, Xi'an 710055, PR China
| | - Xiaohui Tao
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, No. 13 Yanta Road, Xi'an 710055, PR China
| | - Yucong Zheng
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, No. 13 Yanta Road, Xi'an 710055, PR China; International S&T Cooperation Center for Urban Alternative Water Resources Development, Xi'an University of Architecture and Technology, No. 13 Yanta Road, Xi'an 710055, PR China
| | - Xiaochang Wang
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, No. 13 Yanta Road, Xi'an 710055, PR China; International S&T Cooperation Center for Urban Alternative Water Resources Development, Xi'an University of Architecture and Technology, No. 13 Yanta Road, Xi'an 710055, PR China
| | - Rong Chen
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, No. 13 Yanta Road, Xi'an 710055, PR China; International S&T Cooperation Center for Urban Alternative Water Resources Development, Xi'an University of Architecture and Technology, No. 13 Yanta Road, Xi'an 710055, PR China.
| |
Collapse
|