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Jian J, Wang Z, Chen C, Workman CT, Fang X, Larsen TO, Guo J, Sonnenschein EC. Two high-quality Prototheca zopfii genomes provide new insights into their evolution as obligate algal heterotrophs and their pathogenicity. Microbiol Spectr 2024:e0414823. [PMID: 38940543 DOI: 10.1128/spectrum.04148-23] [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: 12/09/2023] [Accepted: 05/24/2024] [Indexed: 06/29/2024] Open
Abstract
The majority of the nearly 10,000 described species of green algae are photoautotrophs; however, some species have lost their ability to photosynthesize and become obligate heterotrophs that rely on parasitism for survival. Two high-quality genomes of the heterotrophic algae Prototheca zopfii Pz20 and Pz23 were obtained using short- and long-read genomic as well as transcriptomic data. The genome sizes were 31.2 Mb and 31.3 Mb, respectively, and contig N50 values of 1.99 Mb and 1.26 Mb. Although P. zopfii maintained its plastid genome, the transition to heterotrophy led to a reduction in both plastid and nuclear genome size, including the loss of photosynthesis-related genes from both the nuclear and plastid genomes and the elimination of genes encoding for carotenoid oxygenase and pheophorbide an oxygenase. The loss of genes, including basic leucine-zipper (bZIP) transcription factors, flavin adenine dinucleotide-linked oxidase, and helicase, could have played a role in the transmission of autotrophy to heterotrophs and in the processes of abiotic stress resistance and pathogenicity. A total of 66 (1.37%) and 73 (1.49%) genes were identified as potential horizontal gene transfer events in the two P. zopfii genomes, respectively. Genes for malate synthase and isocitrate lyase, which are horizontally transferred from bacteria, may play a pivotal role in carbon and nitrogen metabolism as well as the pathogenicity of Prototheca and non-photosynthetic organisms. The two high-quality P. zopfii genomes provide new insights into their evolution as obligate heterotrophs and pathogenicity. IMPORTANCE The genus Prototheca, characterized by its heterotrophic nature and pathogenicity, serves as an exemplary model for investigating pathobiology. The limited understanding of the protothecosis infectious disease is attributed to the lack of genomic resources. Using HiFi long-read sequencing, both nuclear and plastid genomes were generated for two strains of P. zopfii. The findings revealed a concurrent reduction in both plastid and nuclear genome size, accompanied by the loss of genes associated with photosynthesis, carotenoid oxygenase, basic leucine-zipper (bZIP) transcription factors, and others. The analysis of horizontal gene transfer revealed the presence of 1.37% and 1.49% bacterial genes, including malate synthase and isocitrate lyase, which play crucial roles in carbon and nitrogen metabolism, as well as pathogenicity and obligate heterotrophy. The two high-quality P. zopfii genomes represent valuable resources for investigating their adaptation and evolution as obligate heterotrophs, as well as for developing future prevention and treatment strategies against protothecosis.
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Affiliation(s)
- Jianbo Jian
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
- BGI Genomics, Shenzhen, China
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
| | | | | | - Christopher T Workman
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | | | - Thomas Ostenfeld Larsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Jian Guo
- Department of Laboratory Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Eva C Sonnenschein
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
- Department of Biosciences, Swansea University, Swansea, United Kingdom
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Yang B, Vaisvil B, Schmitt D, Collins J, Young E, Kapatral V, Rao R. A correlative study of the genomic underpinning of virulence traits and drug tolerance of Candida auris. Infect Immun 2024; 92:e0010324. [PMID: 38722168 DOI: 10.1128/iai.00103-24] [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: 03/20/2024] [Accepted: 03/22/2024] [Indexed: 06/12/2024] Open
Abstract
Candida auris is an opportunistic fungal pathogen with high mortality rates which presents a clear threat to public health. The risk of C. auris infection is high because it can colonize the body, resist antifungal treatment, and evade the immune system. The genetic mechanisms for these traits are not well known. Identifying them could lead to new targets for new treatments. To this end, we present an analysis of the genetics and gene expression patterns of C. auris carbon metabolism, drug resistance, and macrophage interaction. We chose to study two C. auris isolates simultaneously, one drug sensitive (B11220 from Clade II) and one drug resistant (B11221 from Clade III). Comparing the genomes, we confirm the previously reported finding that B11220 was missing a 12.8 kb region on chromosome VI. This region contains a gene cluster encoding proteins related to alternative sugar utilization. We show that B11221, which has the gene cluster, readily assimilates and utilizes D-galactose and L-rhamnose as compared to B11220, which harbors the deletion. B11221 exhibits increased adherence and drug resistance compared to B11220 when grown in these sugars. Transcriptomic analysis of both isolates grown on glucose or galactose showed that the gene cluster was upregulated when grown on D-galactose. These findings reinforce growing evidence of a link between metabolism and drug tolerance. B11221 resists phagocytosis by macrophages and exhibits decreased β-1,3-glucan exposure, a key determinant that allows Candida to evade the host immune system, as compared to B11220. In a transcriptomic analysis of both isolates co-cultured with macrophages, we find upregulation of genes associated with transport and transcription factors in B11221. Our studies show a positive correlation between membrane composition and immune evasion, alternate sugar utilization, and drug tolerance in C. auris.
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Affiliation(s)
- Bo Yang
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, Massachusetts, USA
| | | | | | - Joseph Collins
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, Massachusetts, USA
| | - Eric Young
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, Massachusetts, USA
| | | | - Reeta Rao
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, Massachusetts, USA
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Xie CY, Su RR, Wu B, Sun ZY, Tang YQ. Response mechanisms of different Saccharomyces cerevisiae strains to succinic acid. BMC Microbiol 2024; 24:158. [PMID: 38720268 PMCID: PMC11077785 DOI: 10.1186/s12866-024-03314-4] [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: 10/27/2023] [Accepted: 04/25/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND The production of succinic acid (SA) from biomass has attracted worldwide interest. Saccharomyces cerevisiae is preferred for SA production due to its strong tolerance to low pH conditions, ease of genetic manipulation, and extensive application in industrial processes. However, when compared with bacterial producers, the SA titers and productivities achieved by engineered S. cerevisiae strains were relatively low. To develop efficient SA-producing strains, it's necessary to clearly understand how S. cerevisiae cells respond to SA. RESULTS In this study, we cultivated five S. cerevisiae strains with different genetic backgrounds under different concentrations of SA. Among them, KF7 and NBRC1958 demonstrated high tolerance to SA, whereas NBRC2018 displayed the least tolerance. Therefore, these three strains were chosen to study how S. cerevisiae responds to SA. Under a concentration of 20 g/L SA, only a few differentially expressed genes were observed in three strains. At the higher concentration of 60 g/L SA, the response mechanisms of the three strains diverged notably. For KF7, genes involved in the glyoxylate cycle were significantly downregulated, whereas genes involved in gluconeogenesis, the pentose phosphate pathway, protein folding, and meiosis were significantly upregulated. For NBRC1958, genes related to the biosynthesis of vitamin B6, thiamin, and purine were significantly downregulated, whereas genes related to protein folding, toxin efflux, and cell wall remodeling were significantly upregulated. For NBRC2018, there was a significant upregulation of genes connected to the pentose phosphate pathway, gluconeogenesis, fatty acid utilization, and protein folding, except for the small heat shock protein gene HSP26. Overexpression of HSP26 and HSP42 notably enhanced the cell growth of NBRC1958 both in the presence and absence of SA. CONCLUSIONS The inherent activities of small heat shock proteins, the levels of acetyl-CoA and the strains' potential capacity to consume SA all seem to affect the responses and tolerances of S. cerevisiae strains to SA. These factors should be taken into consideration when choosing host strains for SA production. This study provides a theoretical basis and identifies potential host strains for the development of robust and efficient SA-producing strains.
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Affiliation(s)
- Cai-Yun Xie
- College of Architecture and Environment, Sichuan University, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan, China
- Sichuan Environmental Protection Key Laboratory of Organic Wastes Valorization, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan, China
- Engineering Research Center of Alternative Energy Materials & Devices, Ministry of Education, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan, China
| | - Ran-Ran Su
- College of Architecture and Environment, Sichuan University, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan, China
- Sichuan Environmental Protection Key Laboratory of Organic Wastes Valorization, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan, China
| | - Bo Wu
- Biogas Institute of Ministry of Agriculture, Renmin Rd. 4-13, Chengdu, 610041, Sichuan, China
| | - Zhao-Yong Sun
- College of Architecture and Environment, Sichuan University, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan, China
- Sichuan Environmental Protection Key Laboratory of Organic Wastes Valorization, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan, China
- Engineering Research Center of Alternative Energy Materials & Devices, Ministry of Education, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan, China
| | - Yue-Qin Tang
- College of Architecture and Environment, Sichuan University, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan, China.
- Sichuan Environmental Protection Key Laboratory of Organic Wastes Valorization, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan, China.
- Engineering Research Center of Alternative Energy Materials & Devices, Ministry of Education, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan, China.
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Raj K, Paul D, Rishi P, Shukla G, Dhotre D, YogeshSouche. Decoding the role of oxidative stress resistance and alternative carbon substrate assimilation in the mature biofilm growth mode of Candida glabrata. BMC Microbiol 2024; 24:128. [PMID: 38641593 PMCID: PMC11031924 DOI: 10.1186/s12866-024-03274-9] [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: 12/31/2023] [Accepted: 03/22/2024] [Indexed: 04/21/2024] Open
Abstract
BACKGROUND Biofilm formation is viewed as a vital mechanism in C. glabrata pathogenesis. Although, it plays a significant role in virulence but transcriptomic architecture and metabolic pathways governing the biofilm growth mode of C. glabrata remain elusive. The present study intended to investigate the genes implicated in biofilm growth phase of C. glabrata through global transcriptomic approach. RESULTS Functional analysis of Differentially expressed genes (DEGs) using gene ontology and pathways analysis revealed that upregulated genes are involved in the glyoxylate cycle, carbon-carbon lyase activity, pre-autophagosomal structure membrane and vacuolar parts whereas, down- regulated genes appear to be associated with glycolysis, ribonucleoside biosynthetic process, ribosomal and translation process in the biofilm growth condition. The RNA-Seq expression of eight selected DEGs (CgICL1, CgMLS1, CgPEP1, and CgNTH1, CgERG9, CgERG11, CgTEF3, and CgCOF1) was performed with quantitative real-time PCR (RT-qPCR). The gene expression profile of selected DEGs with RT-qPCR displayed a similar pattern of expression as observed in RNA-Seq. Phenotype screening of mutant strains generated for genes CgPCK1 and CgPEP1, showed that Cgpck1∆ failed to grow on alternative carbon substrate (Glycerol, Ethanol, Oleic acid) and similarly, Cgpep1∆ unable to grow on YPD medium supplemented with hydrogen peroxide. Our results suggest that in the absence of glucose, C. glabrata assimilate glycerol, oleic acid and generate acetyl coenzyme-A (acetyl-CoA) which is a central and connecting metabolite between catabolic and anabolic pathways (glyoxylate and gluconeogenesis) to produce glucose and fulfil energy requirements. CONCLUSIONS The study was executed using various approaches (transcriptomics, functional genomics and gene deletion) and it revealed that metabolic plasticity of C. glabrata (NCCPF-100,037) in biofilm stage modulates its virulence and survival ability to counter the stress and may promote its transition from commensal to opportunistic pathogen. The observations deduced from the present study along with future work on characterization of the proteins involved in this intricate process may prove to be beneficial for designing novel antifungal strategies.
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Affiliation(s)
- Khem Raj
- Department of Microbiology Basic Medical Sciences Block I, South Campus, Panjab University, Sector-25, Chandigarh, 160014, India.
| | - Dhiraj Paul
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland.
| | - Praveen Rishi
- Department of Microbiology Basic Medical Sciences Block I, South Campus, Panjab University, Sector-25, Chandigarh, 160014, India
| | - Geeta Shukla
- Department of Microbiology Basic Medical Sciences Block I, South Campus, Panjab University, Sector-25, Chandigarh, 160014, India
| | - Dhiraj Dhotre
- National Centre for Microbial Resource, National Centre for Cell Sciences (NCCS), Pune, India
| | - YogeshSouche
- National Centre for Microbial Resource, National Centre for Cell Sciences (NCCS), Pune, India
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Wang S, Meng D, Feng M, Li C, Wang Y. Efficient Plant Triterpenoids Synthesis in Saccharomyces cerevisiae: from Mechanisms to Engineering Strategies. ACS Synth Biol 2024; 13:1059-1076. [PMID: 38546129 DOI: 10.1021/acssynbio.4c00061] [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: 04/20/2024]
Abstract
Triterpenoids possess a range of biological activities and are extensively utilized in the pharmaceutical, food, cosmetic, and chemical industries. Traditionally, they are acquired through chemical synthesis and plant extraction. However, these methods have drawbacks, including high energy consumption, environmental pollution, and being time-consuming. Recently, the de novo synthesis of triterpenoids in microbial cell factories has been achieved. This represents a promising and environmentally friendly alternative to traditional supply methods. Saccharomyces cerevisiae, known for its robustness, safety, and ample precursor supply, stands out as an ideal candidate for triterpenoid biosynthesis. However, challenges persist in industrial production and economic feasibility of triterpenoid biosynthesis. Consequently, metabolic engineering approaches have been applied to improve the triterpenoid yield, leading to substantial progress. This review explores triterpenoids biosynthesis mechanisms in S. cerevisiae and strategies for efficient production. Finally, the review also discusses current challenges and proposes potential solutions, offering insights for future engineering.
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Affiliation(s)
- Shuai Wang
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Dong Meng
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Meilin Feng
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Chun Li
- Key Laboratory for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Ying Wang
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
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6
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Zhang N, Venn B, Bailey CE, Xia M, Mattoon EM, Mühlhaus T, Zhang R. Moderate high temperature is beneficial or detrimental depending on carbon availability in the green alga Chlamydomonas reinhardtii. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:979-1003. [PMID: 37877811 DOI: 10.1093/jxb/erad405] [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: 05/21/2023] [Accepted: 10/21/2023] [Indexed: 10/26/2023]
Abstract
High temperatures impair plant growth and reduce agricultural yields, but the underlying mechanisms remain elusive. The unicellular green alga Chlamydomonas reinhardtii is an excellent model to study heat responses in photosynthetic cells due to its fast growth rate, many similarities in cellular processes to land plants, simple and sequenced genome, and ample genetic and genomics resources. Chlamydomonas grows in light by photosynthesis and with externally supplied acetate as an organic carbon source. Understanding how organic carbon sources affect heat responses is important for the algal industry but remains understudied. We cultivated wild-type Chlamydomonas under highly controlled conditions in photobioreactors at 25 °C (control), 35 °C (moderate high temperature), or 40 °C (acute high temperature) with or without constant acetate supply for 1 or 4 day. Treatment at 35 °C increased algal growth with constant acetate supply but reduced algal growth without sufficient acetate. The overlooked and dynamic effects of 35 °C could be explained by induced acetate uptake and metabolism. Heat treatment at 40 °C for more than 2 day was lethal to algal cultures with or without constant acetate supply. Our findings provide insights to understand algal heat responses and help improve thermotolerance in photosynthetic cells.
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Affiliation(s)
- Ningning Zhang
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Benedikt Venn
- Computational Systems Biology, RPTU Kaiserslautern, 67663 Kaiserslautern, Germany
| | | | - Ming Xia
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Erin M Mattoon
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
- Plant and Microbial Biosciences Program, Division of Biology and Biomedical Sciences, Washington University in Saint Louis, St. Louis, MO 63130, USA
| | - Timo Mühlhaus
- Computational Systems Biology, RPTU Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Ru Zhang
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
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Petrucelli MF, Martins-Santana L, Sanches PR, Oliveira VM, Rossi A, Martinez-Rossi NM. The Transcription Factor StuA Regulates the Glyoxylate Cycle in the Dermatophyte Trichophyton rubrum under Carbon Starvation. Int J Mol Sci 2023; 25:405. [PMID: 38203573 PMCID: PMC10778625 DOI: 10.3390/ijms25010405] [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: 11/11/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 01/12/2024] Open
Abstract
Trichophyton rubrum is the primary causative agent of dermatophytosis worldwide. This fungus colonizes keratinized tissues and uses keratin as a nutritional source during infection. In T. rubrum-host interactions, sensing a hostile environment triggers the adaptation of its metabolic machinery to ensure its survival. The glyoxylate cycle has emerged as an alternative metabolic pathway when glucose availability is limited; this enables the conversion of simple carbon compounds into glucose via gluconeogenesis. In this study, we investigated the impact of stuA deletion on the response of glyoxylate cycle enzymes during fungal growth under varying culture conditions in conjunction with post-transcriptional regulation through alternative splicing of the genes encoding these enzymes. We revealed that the ΔstuA mutant downregulated the malate synthase and isocitrate lyase genes in a keratin-containing medium or when co-cultured with human keratinocytes. Alternative splicing of an isocitrate lyase gene yielded a new isoform. Enzymatic activity assays showed specific instances where isocitrate lyase and malate synthase activities were affected in the mutant strain compared to the wild type strain. Taken together, our results indicate a relevant balance in transcriptional regulation that has distinct effects on the enzymatic activities of malate synthase and isocitrate lyase.
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Affiliation(s)
| | | | | | | | | | - Nilce M. Martinez-Rossi
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, SP, Brazil; (M.F.P.); (L.M.-S.); (P.R.S.); (V.M.O.); (A.R.)
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8
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Lei JD, Li Q, Zhang SB, Lv YY, Zhai HC, Wei S, Ma PA, Hu YS. Transcriptomic and biochemical analyses revealed antifungal mechanism of trans-anethole on Aspergillus flavus growth. Appl Microbiol Biotechnol 2023; 107:7213-7230. [PMID: 37733053 DOI: 10.1007/s00253-023-12791-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/04/2023] [Accepted: 09/12/2023] [Indexed: 09/22/2023]
Abstract
Plant volatile compounds have great potential for preventing and controlling fungal spoilage in post-harvest grains. Recently, we have reported the antifungal effects of trans-anethole, the main volatile constituent of the Illicium verum fruit, on Aspergillus flavus. In this study, the inhibitory mechanisms of trans-anethole against the growth of A. flavus mycelia were investigated using transcriptomic and biochemical analyses. Biochemical and transcriptomic changes in A. flavus mycelia were evaluated after exposure to 0.2 μL/mL trans-anethole. Scanning electron microscopy showed that trans-anethole treatment resulted in the surface wrinkling of A. flavus mycelia, and calcofluor white staining confirmed that trans-anethole treatment disrupted the mycelial cell wall structure. Annexin V-fluorescein isothiocyanate/propidium iodide double staining suggested that trans-anethole induced apoptosis in A. flavus mycelia. Reduced mitochondrial membrane potential and DNA damage were observed in trans-anethole-treated A. flavus mycelia using 5,5',6,6'-tetrachloro-1,1',3,3'-tetraethyl-imidacarbocyanine and 4',6-diamidino-2-phenylindole staining, respectively. 2',7'- Dichloro-dihydro-fluorescein diacetate staining and biochemical assays demonstrated that trans-anethole treatment cause the accumulation of reactive oxygen species in the A. flavus mycelia. Transcriptome results showed that 1673 genes were differentially expressed in A. flavus mycelia exposed to trans-anethole, which were mainly associated with multidrug transport, oxidative phosphorylation, citric acid cycle, ribosomes, and cyclic adenosine monophosphate signaling. We propose that trans-anethole can inhibit the growth of A. flavus mycelia by disrupting the cell wall structure, blocking the multidrug transport process, disturbing the citric acid cycle, and inducing apoptosis. This study provides new insights into the inhibitory mechanism of trans-anethole on A. flavus mycelia and will be helpful for the development of natural fungicides. KEY POINTS: • Biochemical analyses of A. flavus mycelia exposed to trans-anethole were performed • Transcriptomic changes in trans-anethole-treated A. flavus mycelia were analyzed • An inhibitory mechanism of trans-anethole on the growth of A. flavus mycelia was proposed.
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Affiliation(s)
- Jun-Dong Lei
- School of Biological Engineering, Henan University of Technology, 100 Lianhua Street, Zhengzhou, 450001, People's Republic of China
| | - Qiong Li
- School of Biological Engineering, Henan University of Technology, 100 Lianhua Street, Zhengzhou, 450001, People's Republic of China
| | - Shuai-Bing Zhang
- School of Biological Engineering, Henan University of Technology, 100 Lianhua Street, Zhengzhou, 450001, People's Republic of China.
| | - Yang-Yong Lv
- School of Biological Engineering, Henan University of Technology, 100 Lianhua Street, Zhengzhou, 450001, People's Republic of China
| | - Huan-Chen Zhai
- School of Biological Engineering, Henan University of Technology, 100 Lianhua Street, Zhengzhou, 450001, People's Republic of China
| | - Shan Wei
- School of Biological Engineering, Henan University of Technology, 100 Lianhua Street, Zhengzhou, 450001, People's Republic of China
| | - Ping-An Ma
- School of Biological Engineering, Henan University of Technology, 100 Lianhua Street, Zhengzhou, 450001, People's Republic of China
| | - Yuan-Sen Hu
- School of Biological Engineering, Henan University of Technology, 100 Lianhua Street, Zhengzhou, 450001, People's Republic of China
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Lane DM, Valentine DL, Peng X. Genomic analysis of the marine yeast Rhodotorula sphaerocarpa ETNP2018 reveals adaptation to the open ocean. BMC Genomics 2023; 24:695. [PMID: 37986036 PMCID: PMC10662464 DOI: 10.1186/s12864-023-09791-7] [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: 06/29/2023] [Accepted: 11/07/2023] [Indexed: 11/22/2023] Open
Abstract
BACKGROUND Despite a rising interest in the diversity and ecology of fungi in marine environments, there are few published genomes of fungi isolated from the ocean. The basidiomycetous yeast (unicellular fungus) genus Rhodotorula are prevalent and abundant in the open ocean, and they have been isolated from a wide range of other environments. Many of these environments are nutrient poor, such as the Antarctica and the Atacama deserts, raising the question as to how Rhodotorula yeasts may have adapted their metabolic strategies to optimize survival under low nutrient conditions. In order to understand their adaptive strategies in the ocean, the genome of R. sphaerocarpa ETNP2018 was compared to that of fourteen representative Rhodotorula yeasts, isolated from a variety of environments. RESULTS Rhodotorula sphaerocarpa ETNP2018, a strain isolated from the oligotrophic part of the eastern tropical North Pacific (ETNP) oxygen minimum zone (OMZ), hosts the smallest of the fifteen genomes and yet the number of protein-coding genes it possesses is on par with the other strains. Its genome exhibits a distinct reduction in genes dedicated to Major Facilitator Superfamily transporters as well as biosynthetic enzymes. However, its core metabolic pathways are fully conserved. Our research indicates that the selective pressures of the ETNP OMZ favor a streamlined genome with reduced overall biosynthetic potential balanced by a stable set of core metabolisms and an expansion of mechanisms for nutrient acquisition. CONCLUSIONS In summary, this study offers insights into the adaptation of fungi to the oligotrophic ocean and provides valuable information for understanding the ecological roles of fungi in the ocean.
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Affiliation(s)
- Dylan M Lane
- School of Earth, Ocean, and Environment, University of South Carolina, Columbia, SC, USA
| | - David L Valentine
- Marine Science Institute, University of California, Santa Barbara, CA, USA
- Department of Earth Science, University of California, Santa Barbara, CA, USA
| | - Xuefeng Peng
- School of Earth, Ocean, and Environment, University of South Carolina, Columbia, SC, USA.
- Marine Science Institute, University of California, Santa Barbara, CA, USA.
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10
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Nie Z, Wang L, Zhao P, Wang Z, Shi Q, Liu H. Metabolomics reveals the impact of nitrogen combined with the zinc supply on zinc availability in calcareous soil via root exudates of winter wheat (Triticum aestivum). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 204:108069. [PMID: 37852066 DOI: 10.1016/j.plaphy.2023.108069] [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: 05/25/2023] [Revised: 09/25/2023] [Accepted: 09/28/2023] [Indexed: 10/20/2023]
Abstract
A possible mechanism for the improved availability of zinc (Zn) in soil by combining nitrogen (N) with Zn supply was investigated based on the root exudates of winter wheat. N, Zn supply as well as their combination significantly regulated nine root exudates in winter wheat; in which, the secretion of cis-aconitic acid involving in the TCA cycle, C5-branched dibasic acid metabolism, glyoxylate and dicarboxylate metabolism and 2-oxocarboxylic acid metabolism was upregulated by N, Zn supply as well as their combination. N-Zn combination induced the activities of citrate synthase and cis-aconitase in roots and shoots of winter wheat thus to increase the concentrations of citric and aconitic acid; the decrease of isocitric acid concentrations in shoots indicated the inhibited conversion of aconitic acid to isocitric acid by N-Zn combination. It revealed a possible reason for the enhanced secretion of cis-aconitic acid by N-Zn combination. Exogenous addition of 10 μ plant-1 cis-aconitate significantly increased available Zn concentrations in soil and Zn concentrations in winter wheat under N-Zn combination. Thus, the N-Zn combination regulated the metabolism of cis-aconitic acid in winter wheat, thus enhancing the secretion of cis-aconitic acid to increase the bioavailability of Zn in soil.
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Affiliation(s)
- Zhaojun Nie
- Resources and Environment College, Henan Agricultural University, Zhengzhou, 450002, Henan Province, China.
| | - Linglu Wang
- Resources and Environment College, Henan Agricultural University, Zhengzhou, 450002, Henan Province, China.
| | - Peng Zhao
- Resources and Environment College, Henan Agricultural University, Zhengzhou, 450002, Henan Province, China.
| | - Zhenbo Wang
- Resources and Environment College, Henan Agricultural University, Zhengzhou, 450002, Henan Province, China.
| | - Qiuzhe Shi
- Resources and Environment College, Henan Agricultural University, Zhengzhou, 450002, Henan Province, China.
| | - Hongen Liu
- Resources and Environment College, Henan Agricultural University, Zhengzhou, 450002, Henan Province, China.
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11
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Huang YH, Lee YH, Lin CJ, Hsu LH, Chen YL. Deubiquitination module is critical for oxidative stress response and biofilm formation in Candida glabrata. Med Mycol 2023; 61:myad099. [PMID: 37844959 DOI: 10.1093/mmy/myad099] [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: 03/27/2023] [Revised: 09/02/2023] [Accepted: 10/11/2023] [Indexed: 10/18/2023] Open
Abstract
Candidiasis is one of the most important fungal diseases and generally refers to diseases of the skin or mucosal tissues caused by Candida species. Candida glabrata is an opportunistic human fungal pathogen. Infection with C. glabrata has significantly increased due to innate antifungal drug tolerance and the ability to adhere to mucocutaneous surfaces. Spt-Ada-Gcn5 acetyltransferase complex contains two different post-translational modifications, histone acetylation (HAT) module and deubiquitination (DUB) module, which are decisive in gene regulation and highly conserved in eukaryotes. Previous research in our laboratory found that the HAT module ADA2 could regulate C. glabrata oxidative stress tolerance, drug tolerance, cell wall integrity, and virulence. However, the roles of the DUB module that is comprised of UBP8, SGF11, SGF73, and SUS1 genes in those phenotypes are not yet understood. In this study, we found that DUB module genes UBP8, SGF11, and SUS1, but not SGF73 positively regulate histone H2B DUB. Furthermore, ubp8, sgf11, and sus1 mutants exhibited decreased biofilm formation and sensitivity to cell wall-perturbing agent sodium dodecyl sulfate and antifungal drug amphotericin B. In addition, the sgf73 mutant showed increased biofilm formation but was susceptible to oxidative stresses, antifungal drugs, and cell wall perturbing agents. The ubp8, sgf11, and sus1 mutants showed marginal hypovirulence, whereas the sgf73 mutant exhibited virulence similar to the wild type in a murine systemic infection model. In conclusion, the C. glabrata DUB module plays distinct roles in H2B ubiquitination, oxidative stress response, biofilm formation, cell wall integrity, and drug tolerance, but exhibits minor roles in virulence.
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Affiliation(s)
- Yue-Han Huang
- Department of Plant Pathology and Microbiology, National Taiwan University, 10617 Taipei, Taiwan
| | - Yi-Hang Lee
- Department of Plant Pathology and Microbiology, National Taiwan University, 10617 Taipei, Taiwan
| | - Chi-Jan Lin
- Institute of Molecular Biology, National Chung Hsing University, 40227 Taichung, Taiwan
| | - Li-Hang Hsu
- Department of Plant Pathology and Microbiology, National Taiwan University, 10617 Taipei, Taiwan
| | - Ying-Lien Chen
- Department of Plant Pathology and Microbiology, National Taiwan University, 10617 Taipei, Taiwan
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12
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Olanrewaju GO, Kruse CPS, Wyatt SE. Functional Meta-Analysis of the Proteomic Responses of Arabidopsis Seedlings to the Spaceflight Environment Reveals Multi-Dimensional Sources of Variability across Spaceflight Experiments. Int J Mol Sci 2023; 24:14425. [PMID: 37833871 PMCID: PMC10573023 DOI: 10.3390/ijms241914425] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/14/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
The human quest for sustainable habitation of extraterrestrial environments necessitates a robust understanding of life's adaptability to the unique conditions of spaceflight. This study provides a comprehensive proteomic dissection of the Arabidopsis plant's responses to the spaceflight environment through a meta-analysis of proteomics data from four separate spaceflight experiments conducted on the International Space Station (ISS) in different hardware configurations. Raw proteomics LC/MS spectra were analyzed for differential expression in MaxQuant and Perseus software. The analysis of dissimilarities among the datasets reveals the multidimensional nature of plant proteomic responses to spaceflight, impacted by variables such as spaceflight hardware, seedling age, lighting conditions, and proteomic quantification techniques. By contrasting datasets that varied in light exposure, we elucidated proteins involved in photomorphogenesis and skotomorphogenesis in plant spaceflight responses. Additionally, with data from an onboard 1 g control experiment, we isolated proteins that specifically respond to the microgravity environment and those that respond to other spaceflight conditions. This study identified proteins and associated metabolic pathways that are consistently impacted across the datasets. Notably, these shared proteins were associated with critical metabolic functions, including carbon metabolism, glycolysis, gluconeogenesis, and amino acid biosynthesis, underscoring their potential significance in Arabidopsis' spaceflight adaptation mechanisms and informing strategies for successful space farming.
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Affiliation(s)
- Gbolaga O. Olanrewaju
- Molecular and Cellular Biology Program, Ohio University, Athens, OH 45701, USA;
- Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701, USA
| | - Colin P. S. Kruse
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM 87545, USA;
| | - Sarah E. Wyatt
- Molecular and Cellular Biology Program, Ohio University, Athens, OH 45701, USA;
- Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701, USA
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13
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Álvarez-Lugo A, Becerra A. The Fate of Duplicated Enzymes in Prokaryotes: The Case of Isomerases. J Mol Evol 2023; 91:76-92. [PMID: 36580111 DOI: 10.1007/s00239-022-10085-x] [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] [Accepted: 12/16/2022] [Indexed: 12/30/2022]
Abstract
The isomerases are a unique enzymatic class of enzymes that carry out a great diversity of chemical reactions at the intramolecular level. This class comprises about 300 members, most of which are involved in carbohydrate and terpenoid/polyketide metabolism. Along with oxidoreductases and translocases, isomerases are one of the classes with the highest ratio of paralogous enzymes. Due to its relatively small number of members, it is plausible to explore it in greater detail to identify specific cases of gene duplication. Here, we present an analysis at the level of individual isomerases and identify different members that seem to be involved in duplication events in prokaryotes. As was suggested in a previous study, there is no homogeneous distribution of paralogs, but rather they accumulate into a few subcategories, some of which differ between Archaea and Bacteria. As expected, the metabolic processes with more paralogous isomerases have to do with carbohydrate metabolism but also with RNA modification (a particular case involving an rRNA-modifying isomerase is thoroughly discussed and analyzed in detail). Overall, our findings suggest that the most common fate for paralogous enzymes is the retention of the original enzymatic function, either associated with a dosage effect or with differential expression in response to changing environments, followed by subfunctionalization and, to a much lesser degree, neofunctionalization, which is consistent with what has been reported elsewhere.
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Affiliation(s)
- Alejandro Álvarez-Lugo
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City, México.,Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, México
| | - Arturo Becerra
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, México.
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14
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Microbiome Alterations in Alcohol Use Disorder and Alcoholic Liver Disease. Int J Mol Sci 2023; 24:ijms24032461. [PMID: 36768785 PMCID: PMC9916746 DOI: 10.3390/ijms24032461] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 01/22/2023] [Accepted: 01/25/2023] [Indexed: 01/30/2023] Open
Abstract
Microbiome alterations are emerging as one of the most important factors that influence the course of alcohol use disorder (AUD). Recent advances in bioinformatics enable more robust and accurate characterization of changes in the composition of the microbiome. In this study, our objective was to provide the most comprehensive and up-to-date evaluation of microbiome alterations associated with AUD and alcoholic liver disease (ALD). To achieve it, we have applied consistent, state of art bioinformatic workflow to raw reads from multiple 16S rRNA sequencing datasets. The study population consisted of 122 patients with AUD, 75 with ALD, 54 with non-alcoholic liver diseases, and 260 healthy controls. We have found several microbiome alterations that were consistent across multiple datasets. The most consistent changes included a significantly lower abundance of multiple butyrate-producing families, including Ruminococcaceae, Lachnospiraceae, and Oscillospiraceae in AUD compared to HC and further reduction of these families in ALD compared with AUD. Other important results include an increase in endotoxin-producing Proteobacteria in AUD, with the ALD group having the largest increase. All of these alterations can potentially contribute to increased intestinal permeability and inflammation associated with AUD and ALD.
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15
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Similarities and Differences among Species Closely Related to Candida albicans: C. tropicalis, C. dubliniensis, and C. auris. Cell Microbiol 2022. [DOI: 10.1155/2022/2599136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Although Candida species are widespread commensals of the microflora of healthy individuals, they are also among the most important human fungal pathogens that under certain conditions can cause diseases (candidiases) of varying severity ranging from mild superficial infections of the mucous membranes to life-threatening systemic infections. So far, the vast majority of research aimed at understanding the molecular basis of pathogenesis has been focused on the most common species—Candida albicans. Meanwhile, other closely related species belonging to the CTG clade, namely, Candida tropicalis and Candida dubliniensis, are becoming more important in clinical practice, as well as a relatively newly identified species, Candida auris. Despite the close relationship of these microorganisms, it seems that in the course of evolution, they have developed distinct biochemical, metabolic, and physiological adaptations, which they use to fit to commensal niches and achieve full virulence. Therefore, in this review, we describe the current knowledge on C. tropicalis, C. dubliniensis, and C. auris virulence factors, the formation of a mixed species biofilm and mutual communication, the environmental stress response and related changes in fungal cell metabolism, and the effect of pathogens on host defense response and susceptibility to antifungal agents used, highlighting differences with respect to C. albicans. Special attention is paid to common diagnostic problems resulting from similarities between these species and the emergence of drug resistance mechanisms. Understanding the different strategies to achieve virulence, used by important opportunistic pathogens of the genus Candida, is essential for proper diagnosis and treatment.
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16
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Vaughan AL, Altermann E, Glare TR, Hurst MRH. Genome sequence of the entomopathogenic Serratia entomophila isolate 626 and characterisation of the species specific itaconate degradation pathway. BMC Genomics 2022; 23:728. [PMID: 36303123 DOI: 10.1186/s12864-022-08938-2] [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: 03/09/2022] [Accepted: 09/13/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Isolates of Serratia entomophila and S. proteamaculans (Yersiniaceae) cause disease specific to the endemic New Zealand pasture pest, Costelytra giveni (Coleoptera: Scarabaeidae). Previous genomic profiling has shown that S. entomophila isolates appear to have conserved genomes and, where present, conserved plasmids. In the absence of C. giveni larvae, S. entomophila prevalence reduces in the soil over time, suggesting that S. entomophila has formed a host-specific relationship with C. giveni. To help define potential genetic mechanisms driving retention of the chronic disease of S. entomophila, the genome of the isolate 626 was sequenced, enabling the identification of unique chromosomal properties, and defining the gain/loss of accessory virulence factors relevant to pathogenicity to C. giveni larvae. RESULTS We report the complete sequence of S. entomophila isolate 626, a causal agent of amber disease in C. giveni larvae. The genome of S. entomophila 626 is 5,046,461 bp, with 59.1% G + C content and encoding 4,695 predicted CDS. Comparative analysis with five previously sequenced Serratia species, S. proteamaculans 336X, S. marcescens Db11, S. nematodiphila DH-S01, S. grimesii BXF1, and S. ficaria NBRC 102596, revealed a core of 1,165 genes shared. Further comparisons between S. entomophila 626 and S. proteamaculans 336X revealed fewer predicted phage-like regions and genomic islands in 626, suggesting less horizontally acquired genetic material. Genomic analyses revealed the presence of a four-gene itaconate operon, sharing a similar gene order as the Yersinia pestis ripABC complex. Assessment of a constructed 626::RipC mutant revealed that the operon confer a possible metabolic advantage to S. entomophila in the initial stages of C. giveni infection. CONCLUSIONS Evidence is presented where, relative to S. proteamaculans 336X, S. entomophila 626 encodes fewer genomic islands and phages, alluding to limited horizontal gene transfer in S. entomophila. Bioassay assessments of a S. entomophila-mutant with a targeted mutation of the itaconate degradation region unique to this species, found the mutant to have a reduced capacity to replicate post challenge of the C. giveni larval host, implicating the itaconate operon in establishment within the host.
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Affiliation(s)
- Amy L Vaughan
- Bio-Protection Research Centre, Lincoln University, Lincoln, Christchurch, New Zealand. .,AgResearch, Resilient Agriculture, Lincoln Research Centre, Christchurch, New Zealand.
| | - Eric Altermann
- AgResearch, Consumer Interface, Hopkirk Research Centre, Palmerston North, New Zealand.,Riddet Institute, Massey University, Palmerston North, New Zealand
| | - Travis R Glare
- Bio-Protection Research Centre, Lincoln University, Lincoln, Christchurch, New Zealand
| | - Mark R H Hurst
- Bio-Protection Research Centre, Lincoln University, Lincoln, Christchurch, New Zealand.,AgResearch, Resilient Agriculture, Lincoln Research Centre, Christchurch, New Zealand
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17
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Isocitrate binds to the itaconic acid-responsive LysR-type transcriptional regulator RipR in Salmonella pathogenesis. J Biol Chem 2022; 298:102562. [PMID: 36198361 PMCID: PMC9637912 DOI: 10.1016/j.jbc.2022.102562] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 09/25/2022] [Accepted: 09/29/2022] [Indexed: 11/20/2022] Open
Abstract
Macrophages produce itaconic acid in phagosomes in response to bacterial cell wall component lipopolysaccharide to eliminate invading pathogenic bacteria. Itaconic acid competitively inhibits the first enzyme of the bacterial glyoxylate cycle. To overcome itaconic acid stress, bacteria employ the bacterial LysR-type transcriptional regulator RipR. However, it remains unknown which molecule activates RipR in bacterial pathogenesis. In this study, we determined the crystal structure of the regulatory domain of RipR from the intracellular pathogen Salmonella. The RipR regulatory domain structure exhibited the typical dimeric arrangement with the putative ligand-binding site between the two subdomains. Our isothermal titration calorimetry experiments identified isocitrate as the physiological ligand of RipR, whose intracellular level is increased in response to itaconic acid stress. We further found that 3-phenylpropionic acid significantly decreased the resistance of the bacteria to an itaconic acid challenge. Consistently, the complex structure revealed that the compound is antagonistically bound to the RipR ligand-binding site. This study provides the molecular basis of bacterial survival in itaconic acid stress from our immune systems. Further studies are required to reveal biochemical activity, which would elucidate how Salmonella survives in macrophage phagosomes by defending against itaconic acid inhibition of bacterial metabolism.
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18
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Borin GP, Oliveira JVDC. Assessing the intracellular primary metabolic profile of Trichoderma reesei and Aspergillus niger grown on different carbon sources. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:998361. [PMID: 37746225 PMCID: PMC10512294 DOI: 10.3389/ffunb.2022.998361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 08/29/2022] [Indexed: 09/26/2023]
Abstract
Trichoderma reesei and Aspergillus niger are efficient biological platforms for the production of various industrial products, including cellulases and organic acids. Nevertheless, despite the extensive research on these fungi, integrated analyses of omics-driven approaches are still missing. In this study, the intracellular metabolic profile of T. reesei RUT-C30 and A. niger N402 strains grown on glucose, lactose, carboxymethylcellulose (CMC), and steam-exploded sugarcane bagasse (SEB) as carbon sources for 48 h was analysed by proton nuclear magnetic resonance. The aim was to verify the changes in the primary metabolism triggered by these substrates and use transcriptomics data from the literature to better understand the dynamics of the observed alterations. Glucose and CMC induced higher fungal growth whereas fungi grown on lactose showed the lowest dry weight. Metabolic profile analysis revealed that mannitol, trehalose, glutamate, glutamine, and alanine were the most abundant metabolites in both fungi regardless of the carbon source. These metabolites are of particular interest for the mobilization of carbon and nitrogen, and stress tolerance inside the cell. Their concomitant presence indicates conserved mechanisms adopted by both fungi to assimilate carbon sources of different levels of recalcitrance. Moreover, the higher levels of galactose intermediates in T. reesei suggest its better adaptation in lactose, whereas glycolate and malate in CMC might indicate activation of the glyoxylate shunt. Glycerol and 4-aminobutyrate accumulated in A. niger grown on CMC and lactose, suggesting their relevant role in these carbon sources. In SEB, a lower quantity and diversity of metabolites were identified compared to the other carbon sources, and the metabolic changes and higher xylanase and pNPGase activities indicated a better utilization of bagasse by A. niger. Transcriptomic analysis supported the observed metabolic changes and pathways identified in this work. Taken together, we have advanced the knowledge about how fungal primary metabolism is affected by different carbon sources, and have drawn attention to metabolites still unexplored. These findings might ultimately be considered for developing more robust and efficient microbial factories.
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Affiliation(s)
- Gustavo Pagotto Borin
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), São Paulo, Brazil
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas (UNICAMP), São Paulo, Brazil
| | - Juliana Velasco de Castro Oliveira
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), São Paulo, Brazil
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas (UNICAMP), São Paulo, Brazil
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19
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Wang W, Zhao Y, Bai N, Zhang KQ, Yang J. AMPK Is Involved in Regulating the Utilization of Carbon Sources, Conidiation, Pathogenicity, and Stress Response of the Nematode-Trapping Fungus Arthrobotrys oligospora. Microbiol Spectr 2022; 10:e0222522. [PMID: 35916406 PMCID: PMC9431048 DOI: 10.1128/spectrum.02225-22] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/08/2022] [Indexed: 11/20/2022] Open
Abstract
AMP-activated protein kinase (AMPK), a heterotrimeric complex, can sense energy and nutritional status in eukaryotic cells, thereby participating in the regulation of multiple cellular processes. In this study, we characterized the function of the catalytic α-subunit (SNF1) and the two regulatory β- and γ-subunits (GAL83 and SNF4) of AMPK in a representative nematode-trapping fungus, Arthrobotrys oligospora, by gene knockout, phenotypic analysis, and RNA sequencing. The ability of the AMPK complex mutants (including ΔAosnf1, ΔAogal83, and ΔAosnf4) to utilize a nonfermentable carbon source (glycerol) was reduced, and the spore yields and trap formation were remarkably decreased. Moreover, AMPK plays an important role in regulating stress response and nematode predation efficiency. Transcriptomic profiling between the wild-type strain and ΔAosnf1 showed that differentially expressed genes were enriched for peroxisome, endocytosis, fatty acid degradation, and multilipid metabolism (sphingolipid, ether lipid, glycerolipid, and glycerophospholipid). Meanwhile, a reduced lipid droplet accumulation in ΔAosnf1, ΔAogal83, and ΔAosnf4 mutants was observed, and more vacuoles appeared in the mycelia of the ΔAosnf1 mutant. These results highlight the important regulatory role of AMPK in the utilization of carbon sources and lipid metabolism, as well as providing novel insights into the regulatory mechanisms of the mycelia development, conidiation, and trap formation of nematode-trapping (NT) fungi. IMPORTANCE NT fungi are widely distributed in various ecosystems and are important factors in the control of nematode populations in nature; their trophic mycelia can form unique infectious devices (traps) for capturing nematodes. Arthrobotrys oligospora is a representative NT fungi which can develop complex three-dimensional networks (adhesive networks) for nematode predation. Here, we demonstrated that AMPK plays an important role in the glycerol utilization, conidiation, trap formation, and nematode predation of A. oligospora, which was further confirmed by transcriptomic analysis of the wild-type and mutant strains. In particular, our analysis indicated that AMPK is required for lipid metabolism, which is primarily associated with energy regulation and is essential for trap formation. Therefore, this study extends the functional study of AMPK in NT fungi and helps to elucidate the molecular mechanism of the regulation of trap development, as well as laying the foundation for the development of efficient nematode biocontrol agents.
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Affiliation(s)
- Wenjie Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, People’s Republic of China
| | - Yining Zhao
- State Key Laboratory for Conservation and Utilization of Bio-Resources, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, People’s Republic of China
| | - Na Bai
- State Key Laboratory for Conservation and Utilization of Bio-Resources, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, People’s Republic of China
| | - Ke-Qin Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, People’s Republic of China
| | - Jinkui Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, People’s Republic of China
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20
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Ch'ng ACW, Schepergerdes L, Choong YS, Hust M, Lim TS. Antimicrobial antibodies by phage display: Identification of antibody-based inhibitor against mycobacterium tuberculosis isocitrate lyase. Mol Immunol 2022; 150:47-57. [PMID: 35987135 DOI: 10.1016/j.molimm.2022.08.005] [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: 05/13/2022] [Revised: 07/23/2022] [Accepted: 08/09/2022] [Indexed: 10/15/2022]
Abstract
The increasing incidence reports of antibiotic resistance highlights the need for alternative approaches to deal with bacterial infections. This brought about the idea of utilizing monoclonal antibodies as an alternative antibacterial treatment. Majority of the studies are focused on developing antibodies to bacterial surface antigens, with little emphasis on antibodies that inhibit the growth mechanisms of a bacteria host. Isocitrate lyase (ICL) is an important enzyme for the growth and survival of Mycobacterium tuberculosis (MTB) during latent infection as a result of its involvement in the mycobacterial glyoxylate and methylisocitrate cycles. It is postulated that the inhibition of ICL can disrupt the life cycle of MTB. To this extent, we utilized antibody phage display to identify a single chain fragment variable (scFv) antibody against the recombinant ICL protein from MTB. The soluble a-ICL-C6 scFv clone exhibited good binding characteristics with high specificity against ICL. More importantly, the clone exhibited in vitro inhibitory effect with an enzymatic assay resulting in a decrease of ICL enzymatic activity. In silico analysis showed that the scFv-ICL interactions are driven by 23 hydrogen bonds and 13 salt bridges that might disrupt the formation of ICL subunits for the tertiary structure or the formation of active site β domain. However, further validation is necessary to confirm if the isolated clone is indeed a good inhibitor against ICL for application against MTB.
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Affiliation(s)
- Angela Chiew Wen Ch'ng
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Lena Schepergerdes
- Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, 38106 Braunschweig
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Michael Hust
- Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, 38106 Braunschweig
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia; Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11800 Penang, Malaysia.
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21
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Compound Identification from Bromelia karatas Fruit Juice Using Gas Chromatography–Mass Spectrometry and Evaluation of the Bactericidal Activity of the Extract. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12147275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Fruits of species of the genus Bromelia contain compounds with health benefits and potential biotechnological applications. For example, Bromelia karatas fruits contain antioxidants and proteins with bactericidal activity, but studies regarding the activity of these metabolites and potential benefits are required. We evaluated the bactericidal activity of the methanolic extract (treated and not treated with activated charcoal) and its fractions (hexane, ethyl acetate, and methanol) from ripe B. karatas fruit (8 °Brix) against Escherichia coli, Enterococcus faecalis, Salmonella enteritidis, and Shigella flexneri. The methanolic extract (ME) minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) were determined at eight concentrations. The methanolic extract MIC was 5 mg/mL for E. faecalis and 10 mg/mL for the other bacteria; the MBC was 20 mg/mL for E. coli and E. faecalis, and 40 mg/mL for S. enteritidis and S. flexneri. Through gas chromatography–mass spectrometry, 131 compounds were identified, some of which had previously been reported to have biological activities, such as bactericidal, fungicide, anticancer, anti-inflammatory, enzyme inhibiting, and anti-allergic properties. The most abundant compounds found in the ME of B. karatas fruits were maleic anhydride, 5-hydroxymethylfurfural, and itaconic anhydride. This study shows that B. karatas fruits contain metabolites that are potentially beneficial for health.
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22
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Transcriptional changes of biochemical pathways in Meloidogyne incognita in response to non-fumigant nematicides. Sci Rep 2022; 12:9875. [PMID: 35701527 PMCID: PMC9197979 DOI: 10.1038/s41598-022-14091-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 05/17/2022] [Indexed: 11/09/2022] Open
Abstract
Meloidogyne incognita is a destructive and economically important agricultural pest. Similar to other plant-parasitic nematodes, management of M. incognita relies heavily on chemical controls. As old, broad spectrum, and toxic nematicides leave the market, replacements have entered including fluensulfone, fluazaindolizine, and fluopyram that are plant-parasitic nematode specific in target and less toxic to applicators. However, there is limited research into their modes-of-action and other off-target cellular effects caused by these nematicides in plant-parasitic nematodes. This study aimed to broaden the knowledge about these new nematicides by examining the transcriptional changes in M. incognita second-stage juveniles (J2) after 24-h exposure to fluensulfone, fluazaindolizine, and fluopyram as well as oxamyl, an older non-fumigant nematicide. Total RNA was extracted and sequenced using Illumina HiSeq to investigate transcriptional changes in the citric acid cycle, the glyoxylate pathway, [Formula: see text]-fatty acid oxidation pathway, oxidative phosphorylation, and acetylcholine neuron components. Observed transcriptional changes in M. incognita exposed to fluopyram and oxamyl corresponded to their respective modes-of-action. Potential targets for fluensulfone and fluazaindolizine were identified in the [Formula: see text]-fatty acid oxidation pathway and 2-oxoglutarate dehydrogenase of the citric acid cycle, respectively. This study provides a foundation for understanding how potential nematicide resistance could develop, identifies cellular pathways as potential nematicide targets, and determines targets for confirming unknown modes-of-action.
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23
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Xu J, Ren X, Liu Y, Zhang Y, Zhang Y, Chen G, Huang Q, Liu Q, Zhou J, Liu Y. Alterations of Fungal Microbiota in Patients With Cholecystectomy. Front Microbiol 2022; 13:831947. [PMID: 35633725 PMCID: PMC9132483 DOI: 10.3389/fmicb.2022.831947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 03/31/2022] [Indexed: 11/17/2022] Open
Abstract
Increasing evidence suggests a high risk of gastrointestinal postoperative comorbidities (such as colorectal cancer) in patients with postcholecystectomy (PC). Although previous studies implicated the role of fungi in colon carcinogenesis, few reports focused on the fungal profile in patients with PC. We enrolled 104 subjects, including 52 patients with PC and 52 non-PC controls (CON), for fecal collection to detect the fungal composition by an internal transcribed spacer (ITS) 1 rDNA sequencing. Data showed that Candida (C.) glabrata and Aspergillus (A.) Unassigned were enriched, and Candida albicans was depleted in patients with PC. In addition, postoperative duration was the main factor to affect the fungal composition. Machine learning identified that C. glabrata, A. Unassigned, and C. albicans were three biomarkers to discriminate patients with PC from CON subjects. To investigate the fungal role in colon carcinogenesis, the subjects of the PC group were divided into two subgroups, namely, patients with PC without (non-CA) and with precancerous lesions or colorectal cancer (preCA_CRC), by histopathological studies. C. glabrata was found to be gradually accumulated in different statuses of patients with PC. In conclusion, we found fungal dysbiosis in patients with cholecystectomy, and the postoperative duration was a potent factor to influence the fungal composition. The accumulation of C. glabrata might be connected with carcinogenesis after cholecystectomy.
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Affiliation(s)
- Jun Xu
- Department of Gastroenterology, Peking University People's Hospital, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Beijing, China
| | - Xinhua Ren
- Center of Liver Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Yun Liu
- Department of Gastroenterology, Peking University People's Hospital, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Beijing, China
| | - Yuanyuan Zhang
- Department of Gastroenterology, Peking University People's Hospital, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Beijing, China
| | - Yiwen Zhang
- Department of Gastroenterology, Peking University People's Hospital, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Beijing, China
| | - Guodong Chen
- Department of Gastroenterology, Peking University People's Hospital, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Beijing, China
| | - Qing Huang
- Department of Gastroenterology, Peking University People's Hospital, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Beijing, China
| | - Qing Liu
- Department of Gastroenterology, Peking University People's Hospital, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Beijing, China
| | - Jianhua Zhou
- Institute of Clinical Molecular Biology and Central Laboratory, Peking University People's Hospital, Beijing, China
| | - Yulan Liu
- Department of Gastroenterology, Peking University People's Hospital, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Beijing, China
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24
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Transcriptomes analysis of Pichia kudriavzevii UniMAP 3-1 in response to acetic acid supplementation in glucose and xylose medium at elevated fermentation temperature. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.03.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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25
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Miao L, Guo S, Wu J, Adyel TM, Liu Z, Liu S, Hou J. Polystyrene nanoplastics change the functional traits of biofilm communities in freshwater environment revealed by GeoChip 5.0. JOURNAL OF HAZARDOUS MATERIALS 2022; 423:127117. [PMID: 34534802 DOI: 10.1016/j.jhazmat.2021.127117] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 08/17/2021] [Accepted: 08/31/2021] [Indexed: 06/13/2023]
Abstract
There is an increasing concern regarding the potential effects of nanoplastics (NPs) on freshwater ecosystems. Considering the functional values of biofilms in freshwater, knowledge on whether and to what extent NPs can influence the ecosystem processes of biofilms were still limited. Herein, the freshwater biofilms cultured in lab were exposed to 100 nm polystyrene NPs (PS-NPs) of different dosages (1 and 10 mg/L) for 14 days. Confocal laser scanning microscope observation indicated that biofilms were dominated by filamentous, and spiral algae species and the intensity of extracellular polymeric substances increased under PS-NPs exposure. GeoChip 5.0 analysis revealed that PS-NPs exposure triggered a significant increase in functional genes α diversity (p < 0.05) and altered biofilms' functional structure. Furthermore, the abundance of genes involved in the total carbon and nitrogen cycling were increased under PS-NPs exposure. The abundance of nitrogen fixation genes experienced the most pronounced increase (24.4%) under 1 mg/L PS-NPs treatment, consistent with the increase of ammonium in overlying water. Whereas antibiotic resistance genes and those related to photosynthetic pigments production were suppressed. These results provided direct evidence for PS-NPs' effects on the biofilm functions in terms of biogeochemical cycling, improving our understanding of the potentials of NPs on freshwater ecosystems.
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Affiliation(s)
- Lingzhan Miao
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road 1st, Nanjing 210098, People's Republic of China
| | - Song Guo
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, DK-1958 Frederiksberg C, Denmark
| | - Jun Wu
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road 1st, Nanjing 210098, People's Republic of China
| | - Tanveer M Adyel
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Melbourne, VIC 3125, Australia
| | - Zhilin Liu
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road 1st, Nanjing 210098, People's Republic of China
| | - Songqi Liu
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road 1st, Nanjing 210098, People's Republic of China
| | - Jun Hou
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road 1st, Nanjing 210098, People's Republic of China,.
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26
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Role of Cellular Metabolism during Candida-Host Interactions. Pathogens 2022; 11:pathogens11020184. [PMID: 35215128 PMCID: PMC8875223 DOI: 10.3390/pathogens11020184] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 01/19/2022] [Accepted: 01/26/2022] [Indexed: 02/04/2023] Open
Abstract
Microscopic fungi are widely present in the environment and, more importantly, are also an essential part of the human healthy mycobiota. However, many species can become pathogenic under certain circumstances, with Candida spp. being the most clinically relevant fungi. In recent years, the importance of metabolism and nutrient availability for fungi-host interactions have been highlighted. Upon activation, immune and other host cells reshape their metabolism to fulfil the energy-demanding process of generating an immune response. This includes macrophage upregulation of glucose uptake and processing via aerobic glycolysis. On the other side, Candida modulates its metabolic pathways to adapt to the usually hostile environment in the host, such as the lumen of phagolysosomes. Further understanding on metabolic interactions between host and fungal cells would potentially lead to novel/enhanced antifungal therapies to fight these infections. Therefore, this review paper focuses on how cellular metabolism, of both host cells and Candida, and the nutritional environment impact on the interplay between host and fungal cells.
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27
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Vitorino IR, Lage OM. The Planctomycetia: an overview of the currently largest class within the phylum Planctomycetes. Antonie van Leeuwenhoek 2022; 115:169-201. [PMID: 35037113 DOI: 10.1007/s10482-021-01699-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/06/2021] [Indexed: 01/21/2023]
Abstract
The phylum Planctomycetes comprises bacteria with uncommon features among prokaryotes, such as cell division by budding, absence of the bacterial tubulin-homolog cell division protein FtsZ and complex cell plans with invaginations of the cytoplasmic membrane. Although planctomycetes are ubiquitous, the number of described species and isolated strains available as axenic cultures is still low compared to the diversity observed in metagenomes or environmental studies. An increasing interest in planctomycetes is reflected by the recent description of a large number of new species and their increasing accessibility in terms of pure cultures. In this review, data from all taxonomically described species belonging to Planctomycetia, the class with the currently highest number of characterized members within the phylum Planctomycetes, is summarized. Phylogeny, morphology, physiology, ecology and genomic traits of its members are discussed. This comprehensive overview will help to acknowledge several aspects of the biology of these fascinating bacteria.
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Affiliation(s)
- Inês Rosado Vitorino
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal.
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal.
| | - Olga Maria Lage
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal
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28
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Lee J, Heo L, Han SW. Comparative Proteomic Analysis for a Putative Pyridoxal Phosphate-Dependent Aminotransferase Required for Virulence in Acidovorax citrulli. THE PLANT PATHOLOGY JOURNAL 2021; 37:673-680. [PMID: 34897258 PMCID: PMC8666244 DOI: 10.5423/ppj.nt.09.2021.0139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/06/2021] [Accepted: 10/13/2021] [Indexed: 06/14/2023]
Abstract
Acidovorax citrulli (Ac) is the causative agent of bacterial fruit blotch disease in watermelon. Since resistant cultivars have not yet been developed, the virulence factors/mechanisms of Ac need to be characterized. This study reports the functions of a putative pyridoxal phosphate-dependent aminotransferase (PpdaAc) that transfers amino groups to its substrates and uses pyridoxal phosphate as a coenzyme. It was observed that a ppdaAc knockout mutant had a significantly reduced virulence in watermelon when introduced via germinated-seed inoculation as well as leaf infiltration. Comparative proteomic analysis predicted the cellular mechanisms related to PpdaAc. Apart from causing virulence, the PpdaAc may have significant roles in energy production, cell membrane, motility, chemotaxis, post-translational modifications, and iron-related mechanisms. Therefore, it is postulated that PpdaAc may possess pleiotropic effects. These results provide new insights into the functions of a previously unidentified PpdaAc in Ac.
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Affiliation(s)
| | | | - Sang-Wook Han
- Corresponding author: Phone) +82-31-670-3150, FAX) +82-2-670-8845, E-mail)
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29
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Wijnants S, Vreys J, Van Dijck P. Interesting antifungal drug targets in the central metabolism of Candida albicans. Trends Pharmacol Sci 2021; 43:69-79. [PMID: 34756759 DOI: 10.1016/j.tips.2021.10.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/04/2021] [Accepted: 10/05/2021] [Indexed: 01/04/2023]
Abstract
To treat infections caused by Candida albicans, azoles, polyenes, and echinocandins are used. However, resistance occurs against all three, so there is an urgent need for new antifungal drugs with a novel mode of action. Recently, it became clear that central metabolism plays an important role in the virulence of C. albicans. Glycolysis is, for example, upregulated during virulence conditions, whereas the glyoxylate cycle is important upon phagocytosis by host immune cells. These findings indicate that C. albicans adapts its metabolism to the environment for maximal virulence. In this review, we provide an overview of the potency of different central metabolic pathways and their key enzymes as potential antifungal drug targets.
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Affiliation(s)
- Stefanie Wijnants
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, Leuven, Belgium; VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Jolien Vreys
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, Leuven, Belgium; VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Patrick Van Dijck
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, Leuven, Belgium; VIB-KU Leuven Center for Microbiology, Leuven, Belgium.
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30
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Li Q, Liu J, Chen M, Ma K, Wang T, Wu D, Yan G, Wang C, Shao J. Abundance interaction in Candida albicans and Candida glabrata mixed biofilms under diverse conditions. Med Mycol 2021; 59:158-167. [PMID: 32453815 DOI: 10.1093/mmy/myaa040] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 04/08/2020] [Accepted: 04/28/2020] [Indexed: 12/20/2022] Open
Abstract
Candida albicans and Candida glabrata are frequently coisolated from the oral cavity in immunosuppressive or immunocompromised individuals. Their relationship is usually defined as competition as C. glabrata can inhibit growth of C. albicans in cohabitation. In this study, eight C. albicans isolates as well as two C. glabrata strains were used to investigate the effects of culture medium (Roswell Park Memorial Institute [RPMI]-1640, YPD, YND), incubation time (24 h, 48 h, 72 h, 96 h), initial inoculum (C. glabrata: C. albicans = 2:1, 1:1, 1:2), and medium state (static and dynamic states) on viable cell enumeration and relative abundance in both Candida SB and MB. The results showed that in most cases, C. glabrata and C. albicans SB and MB flourished in RPMI-1640 at 24 h under dynamic state compared with other conditions. Except YPD medium, there were high proportions of preponderance of C. albicans over C. glabrata in MB compared with SB. High initial inoculum promoted corresponding Candida number in both SB and MB and its abundance in MB relative to SB. This study revealed an impact of several environmental conditions on the formation of C. albicans and C. glabrata SB and MB and their abundance in MB in comparison with SB, deepening our understanding of both Candida interaction and their resistance mechanism in MB. LAY SUMMARY This study described the effects of diverse experimental conditions on the numbers of Candida albicans and Candida glabrata single biofilms and mixed biofilms and their abundance.
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Affiliation(s)
- Qianqian Li
- Laboratory of Pathogenic Biology and Immunology, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, 436 Room, Zhijing Building, No. 1 Qianjiang Road, Xinzhan District, Hefei 230012, Anhui, China.,Institute of Integrated Traditional Chinese and Western Medicine, Anhui University of Chinese Medicine, Zhijing Building, No. 1 Qianjiang Road, Xinzhan District, Hefei 230012, Anhui, China
| | - Juanjuan Liu
- Laboratory of Pathogenic Biology and Immunology, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, 436 Room, Zhijing Building, No. 1 Qianjiang Road, Xinzhan District, Hefei 230012, Anhui, China.,Institute of Integrated Traditional Chinese and Western Medicine, Anhui University of Chinese Medicine, Zhijing Building, No. 1 Qianjiang Road, Xinzhan District, Hefei 230012, Anhui, China
| | - Mengli Chen
- Laboratory of Pathogenic Biology and Immunology, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, 436 Room, Zhijing Building, No. 1 Qianjiang Road, Xinzhan District, Hefei 230012, Anhui, China.,Institute of Integrated Traditional Chinese and Western Medicine, Anhui University of Chinese Medicine, Zhijing Building, No. 1 Qianjiang Road, Xinzhan District, Hefei 230012, Anhui, China
| | - Kelong Ma
- Laboratory of Pathogenic Biology and Immunology, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, 436 Room, Zhijing Building, No. 1 Qianjiang Road, Xinzhan District, Hefei 230012, Anhui, China.,Institute of Integrated Traditional Chinese and Western Medicine, Anhui University of Chinese Medicine, Zhijing Building, No. 1 Qianjiang Road, Xinzhan District, Hefei 230012, Anhui, China.,Key Laboratory of Xin'An Medicine, Ministry of Education, Anhui University of Chinese Medicine, Xin'An Building, No. 103 Meishan Road, Shushan District, Hefei 230038, Anhui, China.,Anhui Provincial Key Laboratory for Chinese Herbal Compound, Anhui Academy of Chinese Medicine, Hefei 230012, China
| | - Tianming Wang
- Laboratory of Pathogenic Biology and Immunology, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, 436 Room, Zhijing Building, No. 1 Qianjiang Road, Xinzhan District, Hefei 230012, Anhui, China.,Key Laboratory of Xin'An Medicine, Ministry of Education, Anhui University of Chinese Medicine, Xin'An Building, No. 103 Meishan Road, Shushan District, Hefei 230038, Anhui, China.,Anhui Provincial Key Laboratory for Chinese Herbal Compound, Anhui Academy of Chinese Medicine, Hefei 230012, China
| | - Daqiang Wu
- Laboratory of Pathogenic Biology and Immunology, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, 436 Room, Zhijing Building, No. 1 Qianjiang Road, Xinzhan District, Hefei 230012, Anhui, China.,Institute of Integrated Traditional Chinese and Western Medicine, Anhui University of Chinese Medicine, Zhijing Building, No. 1 Qianjiang Road, Xinzhan District, Hefei 230012, Anhui, China.,Key Laboratory of Xin'An Medicine, Ministry of Education, Anhui University of Chinese Medicine, Xin'An Building, No. 103 Meishan Road, Shushan District, Hefei 230038, Anhui, China.,Anhui Provincial Key Laboratory for Chinese Herbal Compound, Anhui Academy of Chinese Medicine, Hefei 230012, China
| | - Guiming Yan
- Laboratory of Pathogenic Biology and Immunology, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, 436 Room, Zhijing Building, No. 1 Qianjiang Road, Xinzhan District, Hefei 230012, Anhui, China.,Key Laboratory of Xin'An Medicine, Ministry of Education, Anhui University of Chinese Medicine, Xin'An Building, No. 103 Meishan Road, Shushan District, Hefei 230038, Anhui, China.,Anhui Provincial Key Laboratory for Chinese Herbal Compound, Anhui Academy of Chinese Medicine, Hefei 230012, China
| | - Changzhong Wang
- Laboratory of Pathogenic Biology and Immunology, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, 436 Room, Zhijing Building, No. 1 Qianjiang Road, Xinzhan District, Hefei 230012, Anhui, China.,Institute of Integrated Traditional Chinese and Western Medicine, Anhui University of Chinese Medicine, Zhijing Building, No. 1 Qianjiang Road, Xinzhan District, Hefei 230012, Anhui, China.,Key Laboratory of Xin'An Medicine, Ministry of Education, Anhui University of Chinese Medicine, Xin'An Building, No. 103 Meishan Road, Shushan District, Hefei 230038, Anhui, China.,Anhui Provincial Key Laboratory for Chinese Herbal Compound, Anhui Academy of Chinese Medicine, Hefei 230012, China
| | - Jing Shao
- Laboratory of Pathogenic Biology and Immunology, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, 436 Room, Zhijing Building, No. 1 Qianjiang Road, Xinzhan District, Hefei 230012, Anhui, China.,Institute of Integrated Traditional Chinese and Western Medicine, Anhui University of Chinese Medicine, Zhijing Building, No. 1 Qianjiang Road, Xinzhan District, Hefei 230012, Anhui, China.,Key Laboratory of Xin'An Medicine, Ministry of Education, Anhui University of Chinese Medicine, Xin'An Building, No. 103 Meishan Road, Shushan District, Hefei 230038, Anhui, China.,Anhui Provincial Key Laboratory for Chinese Herbal Compound, Anhui Academy of Chinese Medicine, Hefei 230012, China
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31
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Hassan Y, Chew SY, Than LTL. Candida glabrata: Pathogenicity and Resistance Mechanisms for Adaptation and Survival. J Fungi (Basel) 2021; 7:jof7080667. [PMID: 34436206 PMCID: PMC8398317 DOI: 10.3390/jof7080667] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/05/2021] [Accepted: 08/05/2021] [Indexed: 02/06/2023] Open
Abstract
Candida glabrata is a yeast of increasing medical relevance, particularly in critically ill patients. It is the second most isolated Candida species associated with invasive candidiasis (IC) behind C. albicans. The attributed higher incidence is primarily due to an increase in the acquired immunodeficiency syndrome (AIDS) population, cancer, and diabetic patients. The elderly population and the frequent use of indwelling medical devices are also predisposing factors. This work aimed to review various virulence factors that facilitate the survival of pathogenic C. glabrata in IC. The available published research articles related to the pathogenicity of C. glabrata were retrieved and reviewed from four credible databases, mainly Google Scholar, ScienceDirect, PubMed, and Scopus. The articles highlighted many virulence factors associated with pathogenicity in C. glabrata, including adherence to susceptible host surfaces, evading host defences, replicative ageing, and producing hydrolytic enzymes (e.g., phospholipases, proteases, and haemolysins). The factors facilitate infection initiation. Other virulent factors include iron regulation and genetic mutations. Accordingly, biofilm production, tolerance to high-stress environments, resistance to neutrophil killings, and development of resistance to antifungal drugs, notably to fluconazole and other azole derivatives, were reported. The review provided evident pathogenic mechanisms and antifungal resistance associated with C. glabrata in ensuring its sustenance and survival.
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Affiliation(s)
- Yahaya Hassan
- Department of Medical Laboratory Science, Faculty of Allied Health Sciences, Bayero University Kano, Kano 700241, Nigeria;
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia;
| | - Shu Yih Chew
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia;
| | - Leslie Thian Lung Than
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia;
- Institute of Bioscience, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia
- Correspondence: ; Tel.: +60-39769-2373
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32
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Lara AC, Corretto E, Kotrbová L, Lorenc F, Petříčková K, Grabic R, Chroňáková A. The Genome Analysis of the Human Lung-Associated Streptomyces sp. TR1341 Revealed the Presence of Beneficial Genes for Opportunistic Colonization of Human Tissues. Microorganisms 2021; 9:microorganisms9081547. [PMID: 34442631 PMCID: PMC8401907 DOI: 10.3390/microorganisms9081547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/12/2021] [Accepted: 07/17/2021] [Indexed: 12/16/2022] Open
Abstract
Streptomyces sp. TR1341 was isolated from the sputum of a man with a history of lung and kidney tuberculosis, recurrent respiratory infections, and COPD. It produces secondary metabolites associated with cytotoxicity and immune response modulation. In this study, we complement our previous results by identifying the genetic features associated with the production of these secondary metabolites and other characteristics that could benefit the strain during its colonization of human tissues (virulence factors, modification of the host immune response, or the production of siderophores). We performed a comparative phylogenetic analysis to identify the genetic features that are shared by environmental isolates and human respiratory pathogens. The results showed a high genomic similarity of Streptomyces sp. TR1341 to the plant-associated Streptomyces sp. endophyte_N2, inferring a soil origin of the strain. Putative virulence genes, such as mammalian cell entry (mce) genes were not detected in the TR1341’s genome. The presence of a type VII secretion system, distinct from the ones found in Mycobacterium species, suggests a different colonization strategy than the one used by other actinomycete lung pathogens. We identified a higher diversity of genes related to iron acquisition and demonstrated that the strain produces ferrioxamine B in vitro. These results indicate that TR1341 may have an advantage in colonizing environments that are low in iron, such as human tissue.
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Affiliation(s)
- Ana Catalina Lara
- Institute of Soil Biology, Biology Centre Academy of Sciences of The Czech Republic, Na Sádkách 702/7, 37005 České Budějovice, Czech Republic; (A.C.L.); (E.C.); (L.K.); (F.L.)
| | - Erika Corretto
- Institute of Soil Biology, Biology Centre Academy of Sciences of The Czech Republic, Na Sádkách 702/7, 37005 České Budějovice, Czech Republic; (A.C.L.); (E.C.); (L.K.); (F.L.)
| | - Lucie Kotrbová
- Institute of Soil Biology, Biology Centre Academy of Sciences of The Czech Republic, Na Sádkách 702/7, 37005 České Budějovice, Czech Republic; (A.C.L.); (E.C.); (L.K.); (F.L.)
| | - František Lorenc
- Institute of Soil Biology, Biology Centre Academy of Sciences of The Czech Republic, Na Sádkách 702/7, 37005 České Budějovice, Czech Republic; (A.C.L.); (E.C.); (L.K.); (F.L.)
| | - Kateřina Petříčková
- Institute of Immunology and Microbiology, 1st Faculty of Medicine, Charles University, Studničkova 7, 12800 Prague 2, Czech Republic;
- Faculty of Science, University of South Bohemia, Branišovská 1645/31a, 37005 České Budějovice, Czech Republic
| | - Roman Grabic
- Faculty of Fisheries and Protection of Waters, University of South Bohemia, Zátiší 728/II, 38925 Vodňany, Czech Republic;
| | - Alica Chroňáková
- Institute of Soil Biology, Biology Centre Academy of Sciences of The Czech Republic, Na Sádkách 702/7, 37005 České Budějovice, Czech Republic; (A.C.L.); (E.C.); (L.K.); (F.L.)
- Correspondence:
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33
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Kwon S, Chun HL, Ha HJ, Lee SY, Park HH. Heterogeneous multimeric structure of isocitrate lyase in complex with succinate and itaconate provides novel insights into its inhibitory mechanism. PLoS One 2021; 16:e0251067. [PMID: 33951112 PMCID: PMC8099091 DOI: 10.1371/journal.pone.0251067] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 04/20/2021] [Indexed: 11/18/2022] Open
Abstract
During the glyoxylate cycle, isocitrate lyases (ICLs) catalyze the lysis of isocitrate to glyoxylate and succinate. Itaconate has been reported to inhibit an ICL from Mycobacterium tuberculosis (tbICL). To elucidate the molecular mechanism of ICL inhibition, we determined the crystal structure of tbICL in complex with itaconate. Unexpectedly, succinate and itaconate were found to bind to the respective active sites in the dimeric form of tbICL. Our structure revealed the active site architecture as an open form, although the substrate and inhibitor were bound to the active sites. Our findings provide novel insights into the conformation of tbICL upon its binding to a substrate or inhibitor, along with molecular details of the inhibitory mechanism of itaconate.
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Affiliation(s)
- Sunghark Kwon
- Department of Biotechnology, Konkuk University, Chungju, Chungbuk, Republic of Korea
| | - Hye Lin Chun
- College of Pharmacy, Chung-Ang University, Dongjak-gu, Seoul, Republic of Korea
| | - Hyun Ji Ha
- College of Pharmacy, Chung-Ang University, Dongjak-gu, Seoul, Republic of Korea
| | - So Yeon Lee
- College of Pharmacy, Chung-Ang University, Dongjak-gu, Seoul, Republic of Korea
| | - Hyun Ho Park
- College of Pharmacy, Chung-Ang University, Dongjak-gu, Seoul, Republic of Korea
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Laurian R, Ravent J, Dementhon K, Lemaire M, Soulard A, Cotton P. Candida albicans Hexokinase 2 Challenges the Saccharomyces cerevisiae Moonlight Protein Model. Microorganisms 2021; 9:microorganisms9040848. [PMID: 33920979 PMCID: PMC8071269 DOI: 10.3390/microorganisms9040848] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/08/2021] [Accepted: 04/11/2021] [Indexed: 12/20/2022] Open
Abstract
Survival of the pathogenic yeast Candida albicans depends upon assimilation of fermentable and non-fermentable carbon sources detected in host microenvironments. Among the various carbon sources encountered in a human body, glucose is the primary source of energy. Its effective detection, metabolism and prioritization via glucose repression are primordial for the metabolic adaptation of the pathogen. In C. albicans, glucose phosphorylation is mainly performed by the hexokinase 2 (CaHxk2). In addition, in the presence of glucose, CaHxK2 migrates in the nucleus and contributes to the glucose repression signaling pathway. Based on the known dual function of the Saccharomyces cerevisiae hexokinase 2 (ScHxk2), we intended to explore the impact of both enzymatic and regulatory functions of CaHxk2 on virulence, using a site-directed mutagenesis approach. We show that the conserved aspartate residue at position 210, implicated in the interaction with glucose, is essential for enzymatic and glucose repression functions but also for filamentation and virulence in macrophages. Point mutations and deletion into the N-terminal region known to specifically affect glucose repression in ScHxk2 proved to be ineffective in CaHxk2. These results clearly show that enzymatic and regulatory functions of the hexokinase 2 cannot be unlinked in C. albicans.
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Affiliation(s)
- Romain Laurian
- INSA Lyon, CNRS, Université de Lyon, Université Claude Bernard Lyon1, UMR5240 MAP, 69622 Villeurbanne, France; (R.L.); (J.R.); (M.L.); (A.S.)
| | - Jade Ravent
- INSA Lyon, CNRS, Université de Lyon, Université Claude Bernard Lyon1, UMR5240 MAP, 69622 Villeurbanne, France; (R.L.); (J.R.); (M.L.); (A.S.)
| | - Karine Dementhon
- UMR-CNRS 5234, Laboratoire de Microbiologie Fondamentale et Pathogénicité, Université de Bordeaux, 33076 Bordeaux, France;
| | - Marc Lemaire
- INSA Lyon, CNRS, Université de Lyon, Université Claude Bernard Lyon1, UMR5240 MAP, 69622 Villeurbanne, France; (R.L.); (J.R.); (M.L.); (A.S.)
| | - Alexandre Soulard
- INSA Lyon, CNRS, Université de Lyon, Université Claude Bernard Lyon1, UMR5240 MAP, 69622 Villeurbanne, France; (R.L.); (J.R.); (M.L.); (A.S.)
| | - Pascale Cotton
- INSA Lyon, CNRS, Université de Lyon, Université Claude Bernard Lyon1, UMR5240 MAP, 69622 Villeurbanne, France; (R.L.); (J.R.); (M.L.); (A.S.)
- Correspondence:
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Liboro K, Yu SR, Lim J, So YS, Bahn YS, Eoh H, Park H. Transcriptomic and Metabolomic Analysis Revealed Roles of Yck2 in Carbon Metabolism and Morphogenesis of Candida albicans. Front Cell Infect Microbiol 2021; 11:636834. [PMID: 33796481 PMCID: PMC8008151 DOI: 10.3389/fcimb.2021.636834] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 02/08/2021] [Indexed: 12/05/2022] Open
Abstract
Candida albicans is a part of the normal microbiome of human mucosa and is able to thrive in a wide range of host environments. As an opportunistic pathogen, the virulence of C. albicans is tied to its ability to switch between yeast and hyphal morphologies in response to various environmental cues, one of which includes nutrient availability. Thus, metabolic flexibility plays an important role in the virulence of the pathogen. Our previous study has shown that C. albicans Yeast Casein Kinase 2 (CaYck2) regulates the yeast-to-hyphal switch, but its regulatory mechanisms remain unknown. This study further elucidated the role of Yck2 in governing morphology and carbon metabolism by analyzing the transcriptome and metabolome of the C. albicans YCK2 deletion mutant strain (yck2Δ strain) in comparison to the wild type strain. Our study revealed that loss of CaYck2 perturbs carbon metabolism, leading to a transcriptional response that resembles a transcriptional response to glucose starvation with coinciding intracellular accumulation of glucose and depletion of TCA cycle metabolites. This shift in the metabolome is likely mediated by derepression of glucose-repressed genes in the Mig1/2-mediated glucose sensing pathway and by downregulation of glycolytic genes, possibly through the Rgt1-mediated SRR pathway. In addition, genes involved in beta-oxidation, glyoxylate cycle, oxidative stress response, and arginine biosynthesis were upregulated in the yck2Δ strain, which is highly reminiscent of C. albicans engulfment by macrophages. This coincides with an increase in arginine degradation intermediates in the yck2Δ strain, suggesting arginine catabolism as a potential mechanism of CaYck2-mediated filamentation as seen during C. albicans escape from macrophages. Transcriptome analysis also shows differential expression of hyphal transcriptional regulators Nrg1 and Ume6. This suggests dysregulation of hyphal initiation and elongation in the yck2Δ strain which may lead to the constitutive pseudohyphal phenotype of this strain. Metabolome analysis also detected a high abundance of methyl citrate cycle intermediates in the yck2Δ strain, suggesting the importance of CaYck2 in this pathway. Taken together, we discovered that CaYck2 is an integral piece of carbon metabolism and morphogenesis of C. albicans.
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Affiliation(s)
- Karl Liboro
- Department of Biological Sciences, California State University, Los Angeles, CA, United States
| | - Seong-Ryong Yu
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Juhyeon Lim
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Yee-Seul So
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Yong-Sun Bahn
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Hyungjin Eoh
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Hyunsook Park
- Department of Biological Sciences, California State University, Los Angeles, CA, United States
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Enriquez-Hesles E, Smith DL, Maqani N, Wierman MB, Sutcliffe MD, Fine RD, Kalita A, Santos SM, Muehlbauer MJ, Bain JR, Janes KA, Hartman JL, Hirschey MD, Smith JS. A cell-nonautonomous mechanism of yeast chronological aging regulated by caloric restriction and one-carbon metabolism. J Biol Chem 2021; 296:100125. [PMID: 33243834 PMCID: PMC7949035 DOI: 10.1074/jbc.ra120.015402] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 10/26/2020] [Accepted: 11/25/2020] [Indexed: 12/30/2022] Open
Abstract
Caloric restriction (CR) improves health span and life span of organisms ranging from yeast to mammals. Understanding the mechanisms involved will uncover future interventions for aging-associated diseases. In budding yeast, Saccharomyces cerevisiae, CR is commonly defined by reduced glucose in the growth medium, which extends both replicative and chronological life span (CLS). We found that conditioned media collected from stationary-phase CR cultures extended CLS when supplemented into nonrestricted (NR) cultures, suggesting a potential cell-nonautonomous mechanism of CR-induced life span regulation. Chromatography and untargeted metabolomics of the conditioned media, as well as transcriptional responses associated with the longevity effect, pointed to specific amino acids enriched in the CR conditioned media (CRCM) as functional molecules, with L-serine being a particularly strong candidate. Indeed, supplementing L-serine into NR cultures extended CLS through a mechanism dependent on the one-carbon metabolism pathway, thus implicating this conserved and central metabolic hub in life span regulation.
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Affiliation(s)
- Elisa Enriquez-Hesles
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Daniel L Smith
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, USA; Department of Nutrition Science, Nathan Shock Center of Excellence in the Basic Biology of Aging, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Nazif Maqani
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Margaret B Wierman
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Matthew D Sutcliffe
- Department of Biomedical Engineering, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Ryan D Fine
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Agata Kalita
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Sean M Santos
- Department of Genetics, Nutrition and Obesity Research Center, Nathan Shock Center of Excellence in the Basic Biology of Aging, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Michael J Muehlbauer
- Department of Medicine, Duke Molecular Physiology Institute, Duke University, Durham, North Carolina, USA
| | - James R Bain
- Department of Medicine, Duke Molecular Physiology Institute, Duke University, Durham, North Carolina, USA
| | - Kevin A Janes
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, USA; Department of Biomedical Engineering, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - John L Hartman
- Department of Genetics, Nutrition and Obesity Research Center, Nathan Shock Center of Excellence in the Basic Biology of Aging, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Matthew D Hirschey
- Department of Medicine, Duke Molecular Physiology Institute, Duke University, Durham, North Carolina, USA
| | - Jeffrey S Smith
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, USA.
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Zhang L, Liu S, Chen Y, Guo J, Li C, Zhang J. Metatranscriptomic approach reveals the functional and enzyme dynamics of core microbes during noni fruit fermentation. Food Res Int 2020; 141:109999. [PMID: 33641950 DOI: 10.1016/j.foodres.2020.109999] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 11/14/2020] [Accepted: 12/08/2020] [Indexed: 01/03/2023]
Abstract
Noni (Morinda citrifolia L.) has been recognized as an important herb for treating various physiological disorders worldwide. Fermented noni fruit juice, established as a novel food in European Union, is the most important noni product. However, the structure, functions and enzyme profiles of microbiome during fermentation remain unclear. The metatranscriptomic was used to comprehensively explore the active microbial community and key metabolic function. Acetobacter sp., Acetobacter aceti and Gluconobacter sp. were the major microorganisms and appeared in succession during fermentation. According to principal components analysis (PCA) of metabolism-related unigenes by KEGG database, the fermentation process was divided into three stages and almost completed at the end of the second stage. Furthermore, carbohydrate-active enzymes (CAZymes) and the expression of key enzymes in major metabolic pathways were analyzed systematically. Analysis by HS-SPME-GC-MS and odor active value (OAV) revealed that butanoic acid and hexanoic acid were the main volatile compounds for the unpleasant odor of fermented noni fruit juice. The microbiome in the fermentation process lacked key enzymes that degrade butanoic acid and hexanoic acid, which imparted rancid and sweat odor. This study provides theoretical basis for product improvement and new product development, thus promoting the development of noni food industry.
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Affiliation(s)
- Lin Zhang
- College of Food Science and Engineering, Hainan University, Haikou 570228, China; School of Life and Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Sixin Liu
- School of Sciences, Hainan University, Haikou 570228, China; Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Haikou 570228, China
| | - Ying Chen
- College of Food Science and Engineering, Hainan University, Haikou 570228, China
| | - Jinbiao Guo
- College of Food Science and Engineering, Hainan University, Haikou 570228, China
| | - Congfa Li
- College of Food Science and Engineering, Hainan University, Haikou 570228, China; Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Haikou 570228, China.
| | - Jiachao Zhang
- College of Food Science and Engineering, Hainan University, Haikou 570228, China; Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Haikou 570228, China.
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Rudowitz M, Erdmann R, Schliebs W. Membrane Processing and Steady-State Regulation of the Alternative Peroxisomal Import Receptor Pex9p. Front Cell Dev Biol 2020; 8:566321. [PMID: 33195197 PMCID: PMC7642143 DOI: 10.3389/fcell.2020.566321] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/30/2020] [Indexed: 01/29/2023] Open
Abstract
Import of peroxisomal matrix proteins with a type 1 peroxisomal targeting signal (PTS1) in Saccharomyces cerevisiae is facilitated by cytosolic import receptors Pex5p and Pex9p. While Pex5p has a broad specificity for all PTS1 proteins independent of the growth conditions, Pex9p is only expressed in fatty-acid containing media to mediate peroxisomal import of the two malate synthases, Mls1p and Mls2p, as well as the glutathione transferase Gto1p. Pex5p-cargo complexes dock at the peroxisomal membrane, translocate their cargo-protein via a transient pore and are recycled into the cytosol for a further round of import. The processing of Pex5p has been shown to require a complex network of interactions with other membrane-bound peroxins, as well as decoration with ubiquitin as signal for its ATP-dependent release and recycling. Here, we show that the alternative receptor Pex9p requires the same set of interacting peroxins to mediate peroxisomal import of Mls1p. However, while Pex5p is rather stable, Pex9p is rapidly degraded during its normal life cycle. The steady-state regulation of Pex9p, combining oleate-induced expression with high turnover rates resembles that of Pex18p, one of the two co-receptors of the PTS2-dependent targeting pathway into peroxisomes. Both Pex9p- and Pex18p-dependent import routes serve the fast metabolic adaptation to changes of carbon sources in baker’s yeast. By sequence similarities, we identified another Pex9p homolog in the human pathogenic fungus Candida glabrata, in which similar metabolic reprogramming strategies are crucial for survival of the pathogen.
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Affiliation(s)
- Markus Rudowitz
- Department of Systems Biochemistry, Institute of Biochemistry and Pathobiochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Ralf Erdmann
- Department of Systems Biochemistry, Institute of Biochemistry and Pathobiochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Wolfgang Schliebs
- Department of Systems Biochemistry, Institute of Biochemistry and Pathobiochemistry, Ruhr-University Bochum, Bochum, Germany
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Oliver JC, Laghi L, Parolin C, Foschi C, Marangoni A, Liberatore A, Dias ALT, Cricca M, Vitali B. Metabolic profiling of Candida clinical isolates of different species and infection sources. Sci Rep 2020; 10:16716. [PMID: 33028931 PMCID: PMC7541501 DOI: 10.1038/s41598-020-73889-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 09/22/2020] [Indexed: 12/27/2022] Open
Abstract
Candida species are the most common cause of opportunistic fungal infections. Rapid identification and novel approaches for the characterization of these fungi are of great interest to improve the diagnosis and the knowledge about their pathogenic properties. This study aimed to characterize clinical isolates of Candida spp. by proteomics (MALDI-TOF MS) and metabolomics (1H-NMR), and to correlate their metabolic profiles with Candida species, source of infection and different virulence associated parameters. In particular, 49 Candida strains from different sources (blood, n = 15; vagina, n = 18; respiratory tract, n = 16), belonging mainly to C. albicans complex (61%), C. glabrata (20%) and C. parapsilosis (12%) species were used. Several extracellular and intracellular metabolites showed significantly different concentrations among isolates recovered from different sources of infection, as well as among different Candida species. These metabolites were mainly related to the glycolysis or gluconeogenesis, tricarboxylic acid cycle, nucleic acid synthesis and amino acid and lipid metabolism. Moreover, we found specific metabolic fingerprints associated with the ability to form biofilm, the antifungal resistance (i.e. caspofungin and fluconazole) and the production of secreted aspartyl proteinase. In conclusion, 1H-NMR-based metabolomics can be useful to deepen Candida spp. virulence and pathogenicity properties.
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Affiliation(s)
- Josidel Conceição Oliver
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, Bologna, Italy
- Department of Microbiology and Immunology, Federal University of Alfenas, Minas Gerais, Brazil
| | - Luca Laghi
- Centre of Foodomics, Department of Agro-Food Science and Technology, Alma Mater Studiorum, University of Bologna, Cesena, Italy
| | - Carola Parolin
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Claudio Foschi
- Microbiology, DIMES, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Antonella Marangoni
- Microbiology, DIMES, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Andrea Liberatore
- Microbiology, DIMES, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | | | - Monica Cricca
- Microbiology, DIMES, Alma Mater Studiorum, University of Bologna, Bologna, Italy.
| | - Beatrice Vitali
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, Bologna, Italy
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Mba IE, Nweze EI. Mechanism of Candida pathogenesis: revisiting the vital drivers. Eur J Clin Microbiol Infect Dis 2020; 39:1797-1819. [PMID: 32372128 DOI: 10.1007/s10096-020-03912-w] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 04/17/2020] [Indexed: 12/14/2022]
Abstract
Candida is the most implicated fungal pathogen in the clinical setting. Several factors play important roles in the pathogenesis of Candida spp. Multiple transcriptional circuits, morphological and phenotypic switching, biofilm formation, tissue damaging extracellular hydrolytic enzymes, metabolic flexibility, genome plasticity, adaptation to environmental pH fluctuation, robust nutrient acquisition system, adherence and invasions (mediated by adhesins and invasins), heat shock proteins (HSPs), cytolytic proteins, escape from phagocytosis, evasion from host immune system, synergistic coaggregation with resident microbiota, resistance to antifungal agents, and the ability to efficiently respond to multiple stresses are some of the major pathogenic determinants of Candida species. The existence of multiple connections, in addition to the interactions and associations among all of these factors, are distinctive features that play important roles in the establishment of Candida infections. This review describes all the underlying factors and mechanisms involved in Candida pathogenesis by evaluating pathogenic determinants of Candida species. It reinforces the already available pool of data on the pathogenesis of Candida species by providing a clear and simplified understanding of the most important factors implicated in the pathogenesis of Candida species. The Candida pathogenesis network, an illustration linking all the major determinants of Candida pathogenesis, is also presented. Taken together, they will further improve our current understanding of how these factors modulate virulence and consequent infection(s). Development of new antifungal drugs and better therapeutic approaches to candidiasis can be achieved in the near future with continuing progress in the understanding of the mechanisms of Candida pathogenesis.
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