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Sood U, Müller M, Lan T, Garg G, Singhvi N, Hira P, Singh P, Nigam A, Verma M, Lata P, Kaur H, Kumar A, Rawat CD, Lal S, Aldrich C, Bechthold A, Lal R. Amycolatopsis mediterranei: A Sixty-Year Journey from Strain Isolation to Unlocking Its Potential of Rifamycin Analogue Production by Combinatorial Biosynthesis. JOURNAL OF NATURAL PRODUCTS 2024; 87:424-438. [PMID: 38289177 DOI: 10.1021/acs.jnatprod.3c00686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Ever since the isolation of Amycolatopsis mediterranei in 1957, this strain has been the focus of research worldwide. In the last 60 years or more, our understanding of the taxonomy, development of cloning vectors and conjugation system, physiology, genetics, genomics, and biosynthetic pathway of rifamycin B production in A. mediterranei has substantially increased. In particular, the development of cloning vectors, transformation system, characterization of the rifamycin biosynthetic gene cluster, and the regulation of rifamycin B production by the pioneering work of Heinz Floss have made the rifamycin polyketide biosynthetic gene cluster (PKS) an attractive target for extensive genetic manipulations to produce rifamycin B analogues which could be effective against multi-drug-resistant tuberculosis. Additionally, a better understanding of the regulation of rifamycin B production and the application of newer genomics tools, including CRISPR-assisted genome editing systems, might prove useful to overcome the limitations associated with low production of rifamycin analogues.
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Affiliation(s)
- Utkarsh Sood
- Department of Zoology, Kirori Mal College, University of Delhi, Delhi-110007, India
| | - Moritz Müller
- Institute of Pharmaceutical Biology and Biotechnology, Albert-Ludwigs-Universität, Stefan-Meier-Straße 19, 79104, Freiburg, Germany
| | - Tian Lan
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Gauri Garg
- Department of Zoology, Kirori Mal College, University of Delhi, Delhi-110007, India
| | - Nirjara Singhvi
- School of Allied Sciences, Dev Bhoomi Uttarakhand University, Dehradun, Uttarakhand 248007, India
| | - Princy Hira
- Department of Zoology, Maitreyi College, University of Delhi, Delhi-110003, India
| | - Priya Singh
- Department of Zoology, Maitreyi College, University of Delhi, Delhi-110003, India
| | - Aeshna Nigam
- Department of Zoology, Shivaji College, University of Delhi, Delhi-110027, India
| | - Mansi Verma
- Department of Zoology, Hansraj College, University of Delhi, Delhi-110007, India
| | - Pushp Lata
- Department of Zoology, University of Delhi, Delhi-110007, India
| | - Hardeep Kaur
- Department of Zoology, Ramjas College, University of Delhi, Delhi-110007, India
| | - Abhilash Kumar
- Department of Zoology, Ramjas College, University of Delhi, Delhi-110007, India
| | - Charu Dogra Rawat
- Department of Zoology, Ramjas College, University of Delhi, Delhi-110007, India
| | - Sukanya Lal
- PhiXGen Private Limited, Gurugram, Haryana-122001, India
| | - Courtney Aldrich
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Andreas Bechthold
- Institute of Pharmaceutical Biology and Biotechnology, Albert-Ludwigs-Universität, Stefan-Meier-Straße 19, 79104, Freiburg, Germany
| | - Rup Lal
- PhiXGen Private Limited, Gurugram, Haryana-122001, India
- Acharya Narendra Dev College, University of Delhi, Delhi-110019, India
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2
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Kaszab E, Jiang D, Szabó I, Kriszt B, Urbányi B, Szoboszlay S, Sebők R, Bock I, Csenki-Bakos Z. Evaluating the In Vivo Virulence of Environmental Pseudomonas aeruginosa Using Microinjection Model of Zebrafish ( Danio rerio). Antibiotics (Basel) 2023; 12:1740. [PMID: 38136774 PMCID: PMC10740789 DOI: 10.3390/antibiotics12121740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/10/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023] Open
Abstract
(1) Background: Microinjection of zebrafish (Danio rerio) embryos offers a promising model for studying the virulence and potential environmental risks associated with Pseudomonas aeruginosa. (2) Methods: This work aimed to develop a P. aeruginosa infection model using two parallel exposition pathways on zebrafish larvae with microinjection into the yolk and the perivitelline space to simultaneously detect the invasive and cytotoxic features of the examined strains. The microinjection infection model was validated with 15 environmental and clinical strains of P. aeruginosa of various origins, antibiotic resistance profiles, genotypes and phenotypes: both exposition pathways were optimized with a series of bacterial dilutions, different drop sizes (injection volumes) and incubation periods. Besides mortality, sublethal symptoms of the treated embryos were detected and analyzed. (3) Results: According to the statistical evaluation of our results, the optimal parameters (dilution, drop size and incubation period) were determined. (4) Conclusions: The tested zebrafish embryo microinjection infection model is now ready for use to determine the in vivo virulence and ecological risk of environmental P. aeruginosa.
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Affiliation(s)
- Edit Kaszab
- Department of Environmental Safety, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, 2100 Gödöllő, Hungary; (E.K.); (D.J.); (S.S.); (R.S.)
| | - Dongze Jiang
- Department of Environmental Safety, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, 2100 Gödöllő, Hungary; (E.K.); (D.J.); (S.S.); (R.S.)
| | - István Szabó
- Department of Environmental Toxicology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, 2100 Gödöllő, Hungary; (I.S.); (I.B.); (Z.C.-B.)
| | - Balázs Kriszt
- Department of Environmental Safety, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, 2100 Gödöllő, Hungary; (E.K.); (D.J.); (S.S.); (R.S.)
| | - Béla Urbányi
- Department of Aquaculture, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, 2100 Gödöllő, Hungary;
| | - Sándor Szoboszlay
- Department of Environmental Safety, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, 2100 Gödöllő, Hungary; (E.K.); (D.J.); (S.S.); (R.S.)
| | - Rózsa Sebők
- Department of Environmental Safety, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, 2100 Gödöllő, Hungary; (E.K.); (D.J.); (S.S.); (R.S.)
| | - Illés Bock
- Department of Environmental Toxicology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, 2100 Gödöllő, Hungary; (I.S.); (I.B.); (Z.C.-B.)
| | - Zsolt Csenki-Bakos
- Department of Environmental Toxicology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, 2100 Gödöllő, Hungary; (I.S.); (I.B.); (Z.C.-B.)
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3
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Quiroz-Morales SE, Muriel-Millán LF, Ponce-Soto GY, González-Valdez A, Castillo-Juárez I, Servín-González L, Soberón-Chávez G. Pseudomonas aeruginosa strains belonging to phylogroup 3 frequently exhibit an atypical quorum sensing response: the case of MAZ105, a tomato rhizosphere isolate. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001401. [PMID: 37819040 PMCID: PMC10634362 DOI: 10.1099/mic.0.001401] [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: 03/22/2023] [Accepted: 10/03/2023] [Indexed: 10/13/2023]
Abstract
Pseudomonas aeruginosa is a widespread γ-proteobacterium and an important opportunistic pathogen. The genetically diverse P. aeruginosa phylogroup 3 strains are characterized by producing the pore-forming ExlA toxin and by their lack of a type III secretion system. However, like all strains of this species, they produce several virulence-associated traits, such as elastase, rhamnolipids and pyocyanin, which are regulated by quorum sensing (QS). The P. aeruginosa QS response comprises three systems (Las, Rhl and Pqs, respectively) that hierarchically regulate these virulence factors. The Pqs QS system is composed of the PqsR transcriptional factor, which, coupled with the alkyl-quinolones HHQ or PQS, activates the transcription of the pqsABCDE operon. The products of the first four genes of this operon produce HHQ, which is then converted to PQS by PqsH, while PqsE forms a complex with RhlR and stabilizes it. In this study we report that mutations affecting the Pqs system are particularly common in phylogroup 3 strains. To better understand QS in phylogroup 3 strains we studied strain MAZ105 isolated from tomato rhizosphere and showed that it contains mutations in the central QS transcriptional regulator, LasR, and in the gene encoding the PqsA enzyme involved in the synthesis of PQS. However, it can still produce QS-regulated virulence factors and is virulent in Galleria mellonella and mildly pathogenic in the mouse abscess/necrosis model; our results show that this may be due to the expression of pqsE from a different PqsR-independent promoter than the pqsA promoter. Our results indicate that using anti-virulence therapy based on targeting the PQS system will not be effective against infections by P. aeruginosa phylogroup 3 strains.
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Affiliation(s)
- Sara E. Quiroz-Morales
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apdo, Postal 70228, C. P. 04510, CDMX, Mexico
| | - Luis Felipe Muriel-Millán
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos CP 62210, Mexico
| | - Gabriel Y. Ponce-Soto
- Microbial Paleogenomics Unit, Department of Genomes and Genetics, Pasteur Institute, 75015 Paris, France
| | - Abigail González-Valdez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apdo, Postal 70228, C. P. 04510, CDMX, Mexico
| | - Israel Castillo-Juárez
- Laboratorio de Investigación y Aplicación de Fitoquímicos Bioactivos, Colegio de Postgraduados, 56230, Campus Montecillo, Texcoco, Mexico
| | - Luis Servín-González
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apdo, Postal 70228, C. P. 04510, CDMX, Mexico
| | - Gloria Soberón-Chávez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apdo, Postal 70228, C. P. 04510, CDMX, Mexico
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4
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Caliskan M, Poschmann G, Gudzuhn M, Waldera-Lupa D, Molitor R, Strunk CH, Streit WR, Jaeger KE, Stühler K, Kovacic F. Pseudomonas aeruginosa responds to altered membrane phospholipid composition by adjusting the production of two-component systems, proteases and iron uptake proteins. Biochim Biophys Acta Mol Cell Biol Lipids 2023; 1868:159317. [PMID: 37054907 DOI: 10.1016/j.bbalip.2023.159317] [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: 12/24/2022] [Revised: 03/16/2023] [Accepted: 03/21/2023] [Indexed: 04/15/2023]
Abstract
Membrane protein and phospholipid (PL) composition changes in response to environmental cues and during infections. To achieve these, bacteria use adaptation mechanisms involving covalent modification and remodelling of the acyl chain length of PLs. However, little is known about bacterial pathways regulated by PLs. Here, we investigated proteomic changes in the biofilm of P. aeruginosa phospholipase mutant (∆plaF) with altered membrane PL composition. The results revealed profound alterations in the abundance of many biofilm-related two-component systems (TCSs), including accumulation of PprAB, a key regulator of the transition to biofilm. Furthermore, a unique phosphorylation pattern of transcriptional regulators, transporters and metabolic enzymes, as well as differential production of several proteases, in ∆plaF, indicate that PlaF-mediated virulence adaptation involves complex transcriptional and posttranscriptional response. Moreover, proteomics and biochemical assays revealed the depletion of pyoverdine-mediated iron uptake pathway proteins in ∆plaF, while proteins from alternative iron-uptake systems were accumulated. These suggest that PlaF may function as a switch between different iron-acquisition pathways. The observation that PL-acyl chain modifying and PL synthesis enzymes were overproduced in ∆plaF reveals the interconnection of degradation, synthesis and modification of PLs for proper membrane homeostasis. Although the precise mechanism by which PlaF simultaneously affects multiple pathways remains to be elucidated, we suggest that alteration of PL composition in ∆plaF plays a role for the global adaptive response in P. aeruginosa mediated by TCSs and proteases. Our study revealed the global regulation of virulence and biofilm by PlaF and suggests that targeting this enzyme may have therapeutic potential.
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Affiliation(s)
- Muttalip Caliskan
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Jülich, Germany
| | - Gereon Poschmann
- Institute of Molecular Medicine, Proteome Research, University Hospital and Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Mirja Gudzuhn
- Department of Microbiology and Biotechnology, University of Hamburg, Ohnhorststr. 18, 22609 Hamburg, Germany
| | - Daniel Waldera-Lupa
- Institute of Molecular Medicine, Proteome Research, University Hospital and Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Rebecka Molitor
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Jülich, Germany
| | | | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, University of Hamburg, Ohnhorststr. 18, 22609 Hamburg, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Jülich, Germany; Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Kai Stühler
- Institute of Molecular Medicine, Proteome Research, University Hospital and Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany; Molecular Proteomics Laboratory, Biologisch-Medizinisches Forschungszentrum, Heinrich-Heine-University, Düsseldorf, Düsseldorf, Germany
| | - Filip Kovacic
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Jülich, Germany.
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5
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Klockgether J, Pust MM, Davenport CF, Bunk B, Spröer C, Overmann J, Tümmler B. Structural genome variants of Pseudomonas aeruginosa clone C and PA14 strains. Front Microbiol 2023; 14:1095928. [PMID: 36992927 PMCID: PMC10040652 DOI: 10.3389/fmicb.2023.1095928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 02/20/2023] [Indexed: 03/16/2023] Open
Abstract
Plasticity of Pseudomonas aeruginosa chromosomes is mainly driven by an extended accessory genome that is shaped by insertion and deletion events. Further modification of the genome composition can be induced by chromosomal inversion events which lead to relocation of genes in the affected genomic DNA segments, modify the otherwise highly conserved core genome synteny and could even alter the location of the replication terminus. Although the genome of the first sequenced strain, PAO1, displayed such a large genomic inversion, knowledge on such recombination events in the P. aeruginosa population is limited. Several large inversions had been discovered in the late 1990s in cystic fibrosis isolates of the major clonal lineage C by physical genome mapping, and subsequent work on these examples led to the characterization of the DNA at the recombination breakpoints and a presumed recombination mechanism. Since then, the topic was barely addressed in spite of the compilation of thousands of P. aeruginosa genome sequences that are deposited in databases. Due to the use of second-generation sequencing, genome contig assembly had usually followed synteny blueprints provided by the existing reference genome sequences. Inversion detection was not feasible by these approaches, as the respective read lengths did not allow reliable resolution of sequence repeats that are typically found at the borders of inverted segments. In this study, we applied PacBio and MinION long-read sequencing to isolates of the mentioned clone C collection. Confirmation of inversions predicted from the physical mapping data demonstrated that unbiased sequence assembly of such read datasets allows the detection of genomic inversions and the resolution of the recombination breakpoint regions. Additional long-read sequencing of representatives of the other major clonal lineage, PA14, revealed large inversions in several isolates, from cystic fibrosis origin as well as from other sources. These findings indicated that inversion events are not restricted to strains from chronic infection background, but could be widespread in the P. aeruginosa population and contribute to genome plasticity. Moreover, the monitored examples emphasized the role of small mobile DNA units, such as IS elements or transposons, and accessory DNA elements in the inversion-related recombination processes.
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Affiliation(s)
- Jens Klockgether
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hanover, Germany
- *Correspondence: Jens Klockgether,
| | - Marie-Madlen Pust
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hanover, Germany
| | - Colin F. Davenport
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hanover, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jörg Overmann
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- German Center for Infection Research, Partner Site Hannover-Braunschweig, Braunschweig, Germany
| | - Burkhard Tümmler
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hanover, Germany
- German Center for Lung Research, Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Hannover Medical School, Hanover, Germany
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Jiang J, Guo X, Tan H, Ding M, Liu F, Yang Z, Zhu J. Transcriptome sequencing leads to an improved understanding of the infection mechanism of Alternaria solani in potato. BMC PLANT BIOLOGY 2023; 23:120. [PMID: 36859112 PMCID: PMC9976505 DOI: 10.1186/s12870-023-04103-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Alternaria solani (A. solani), the main pathogen of potato early blight, causes serious yield reductions every year. The application of fungicides is the most common and effective method of controlling Alternaria-caused diseases. The differentially expressed transcripts of A. solani infecting potato were identified, revealing a group of valuable candidate genes for a systematic analysis to increase the understanding of the molecular pathogenesis of A. solani, and providing scientific data for formulating additional measures to prevent and control potato early blight. In this study, a deep RNA-sequencing approach was applied to gain insights into A. solani pathogenesis. At 3, 4, and 5 days post inoculation (dpi), RNA samples from the susceptible potato cultivar Favorita infected with A. solani strain HWC-168, were sequenced and utilized for transcriptome analysis, and compared to the transcriptome obtained 0 dpi. RESULTS A total of 4430 (2167 upregulated, 2263 downregulated), 4736 (2312 upregulated, 2424 downregulated), and 5043 (2411 upregulated, 2632 downregulated) genes were differentially expressed 3, 4 and 5 dpi, respectively, compared with genes analysed at 0 dpi. KEGG enrichment analysis showed that genes involved in the pathways of amino acid metabolism, glucose metabolism, and enzyme activity were significantly differentially expressed at the late infection stage. Correspondingly, symptoms developed rapidly during the late stage of A. solani infection. In addition, a short time-series expression miner (STEM) assay was performed to analyse the gene expression patterns of A. solani and Profile 17 and 19 showed significant change trends 3, 4 and 5 dpi. Both profiles, but especially Profile 17, included enzymes, including transferases, oxidoreductases, hydrolases and carbohydrate-active enzymes (CAZYmes), which may play important roles in late fungal infection. Furthermore, possible candidate effectors were identified through the adopted pipelines, with 137 differentially expressed small secreted proteins identified, including some enzymes and proteins with unknown functions. CONCLUSIONS Collectively, the data presented in this study show that amino acid metabolism, and glucose metabolism pathways, and specific pathway-related enzymes may be key putative pathogenic factors, and play important roles in late stage A. solani infection. These results contribute to a broader base of knowledge of A. solani pathogenesis in potato, as indicated by the transcriptional level analysis, and provide clues for determining the effectors of A. solani infection.
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Affiliation(s)
- Jia Jiang
- College of Plant Protection, Hebei Agricultural University, Baoding, 071001, China
- Department of Plant Protection, College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, China
| | - Xuhao Guo
- Department of Plant Protection, College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, China
| | - Huanhuan Tan
- Department of Plant Protection, College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, China
| | - Mingya Ding
- Potato Research Institute of Weichang Manchu and Mongolian Autonomous County, Chengde, 068450, China
| | - Fangming Liu
- Potato Research Institute of Weichang Manchu and Mongolian Autonomous County, Chengde, 068450, China
| | - Zhihui Yang
- College of Plant Protection, Hebei Agricultural University, Baoding, 071001, China
| | - Jiehua Zhu
- College of Plant Protection, Hebei Agricultural University, Baoding, 071001, China.
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Rudra B, Duncan L, Shah AJ, Shah HN, Gupta RS. Phylogenomic and comparative genomic studies robustly demarcate two distinct clades of Pseudomonas aeruginosa strains: proposal to transfer the strains from an outlier clade to a novel species Pseudomonas paraeruginosa sp. nov. Int J Syst Evol Microbiol 2022; 72. [PMID: 36355412 DOI: 10.1099/ijsem.0.005542] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The strains of
Pseudomonas aeruginosa
exhibit considerable differences in their genotypic and pathogenic properties. To clarify their evolutionary/taxonomic relationships, comprehensive phylogenomic and comparative genomic studies were conducted on the genome sequences of 212
P
.
aeruginosa
strains covering their genetic diversity. In a phylogenomic tree based on 118 conserved proteins, the analysed strains formed two distinct clades. One of these clades, Clade-1, encompassing >70 % of the strains including the type strain DSM 50071T, represents the species P. aeruginosa sensu stricto. Clade-2, referred to in earlier work as the outlier group, with NCTC 13628T as its type strain, constitutes a novel species level lineage. The average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization values between the strains from Clade-1 and Clade-2 are in the range of 93.4–93.7, 95.1–95.3 and 52–53 %, respectively. The 16S rRNA gene of
P. aeruginosa
DSM 50071T also shows 98.3 % similarity to that of NCTC 13628T. These values are lower than the suggested cut-off values for species distinction, indicating that the Clade-2 strains (NCTC 13628T) constitute a new species. We also report the identification of 12 conserved signature indels in different proteins and 24 conserved signature proteins that are exclusively found in either Clade-1 or Clade-2, providing a reliable means for distinguishing these clades. Additionally, in contrast to swimming motility, twitching motility is only present in Clade-1 strains. Based on earlier work, the strains from these two clades also differ in their pathogenic mechanisms (presence/absence of Type III secretion system), production of biosurfactants, phenazines and siderophores, and several other genomic characteristics. Based on the evidence from different studies, we propose that the Clade-2 strains constitute a novel species for which the name Pseudomonas paraeruginosa is proposed. The type strain is NCTC 13628T (=PA7T=ATCC 9027T). The description of
Pseudomonas aeruginosa
is also emended to include information for different molecular markers specific for this species.
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Affiliation(s)
- Bashudev Rudra
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton L8N 3Z5, Canada
| | - Louise Duncan
- School of Cancer and Pharmaceutical Sciences, King's College London, London SE1 9NH, UK
| | - Ajit J Shah
- Department of Natural Sciences, Middlesex University, London NW4 4BT, UK
| | - Haroun N Shah
- Department of Natural Sciences, Middlesex University, London NW4 4BT, UK
| | - Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton L8N 3Z5, Canada
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8
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Huber P. ExlA: A New Contributor to Pseudomonas aeruginosa Virulence. Front Cell Infect Microbiol 2022; 12:929150. [PMID: 35811671 PMCID: PMC9260685 DOI: 10.3389/fcimb.2022.929150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 05/19/2022] [Indexed: 11/17/2022] Open
Abstract
ExlA (also called exolysin) is a recently discovered virulence factor secreted by a subset of Pseudomonas aeruginosa strains in which a type 3 secretion system is lacking. exlA-positive strains were identified worldwide in the clinic, causing several types of infectious diseases, and were detected in various locations in the environment. ExlA possesses pore-forming activity and is cytolytic for most human cell types. It belongs to a class of poorly characterized bacterial toxins, sharing a similar protein domain organization and a common secretion pathway. This review summarizes the recent findings regarding ExlA synthesis, its secretion pathway, and its toxic behavior for host cells.
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9
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Zhang M, Li A, Yao Q, Xiao B, Zhu H. Pseudomonas oligotrophica sp. nov., a Novel Denitrifying Bacterium Possessing Nitrogen Removal Capability Under Low Carbon–Nitrogen Ratio Condition. Front Microbiol 2022; 13:882890. [PMID: 35668762 PMCID: PMC9164167 DOI: 10.3389/fmicb.2022.882890] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 04/25/2022] [Indexed: 01/02/2023] Open
Abstract
Pseudomonas is a large and diverse genus within the Gammaproteobacteria known for its important ecological role in the environment. These bacteria exhibit versatile features of which the ability of heterotrophic nitrification and aerobic denitrification can be applied for nitrogen removal from the wastewater. A novel denitrifying bacterium, designated JM10B5aT, was isolated from the pond water for juvenile Litopenaeus vannamei. The phylogenetic, genomic, physiological, and biochemical analyses illustrated that strain JM10B5aT represented a novel species of the genus Pseudomonas, for which the name Pseudomonas oligotrophica sp. nov. was proposed. The effects of carbon sources and C/N ratios on denitrification performance of strain JM10B5aT were investigated. In addition, the results revealed that sodium acetate was selected as the optimum carbon source for denitrification of this strain. Besides, strain JM10B5aT could exhibit complete nitrate removal at the low C/N ratio of 3. Genomic analyses revealed that JM10B5aT possessed the functional genes including napA, narG, nirS, norB, and nosZ, which might participate in the complete denitrification process. Comparative genomic analyses indicated that many genes related to aggregation, utilization of alkylphosphonate and tricarballylate, biosynthesis of cofactors, and vitamins were contained in the genome of strain JM10B5aT. These genomic features were indicative of its adaption to various niches. Moreover, strain JM10B5aT harbored the complete operons required for the biosynthesis of vibrioferrin, a siderophore, which might be conducive to the high denitrification efficiency of denitrifying bacterium at low C/N ratio. Our findings demonstrated that the strain JM10B5aT could be a promising candidate for treating wastewater with a low C/N ratio.
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Affiliation(s)
- Mingxia Zhang
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School Biology and Biological Engineering, South China University of Technology, Guangzhou, China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Anzhang Li
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- Guangdong BOWOTE BioSciTech, Co., Ltd., Zhaoqing, China
| | - Qing Yao
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Botao Xiao
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School Biology and Biological Engineering, South China University of Technology, Guangzhou, China
- Botao Xiao
| | - Honghui Zhu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- *Correspondence: Honghui Zhu
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10
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Hyun JC, Monk JM, Palsson BO. Comparative pangenomics: analysis of 12 microbial pathogen pangenomes reveals conserved global structures of genetic and functional diversity. BMC Genomics 2022; 23:7. [PMID: 34983386 PMCID: PMC8725406 DOI: 10.1186/s12864-021-08223-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/20/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND With the exponential growth of publicly available genome sequences, pangenome analyses have provided increasingly complete pictures of genetic diversity for many microbial species. However, relatively few studies have scaled beyond single pangenomes to compare global genetic diversity both within and across different species. We present here several methods for "comparative pangenomics" that can be used to contextualize multi-pangenome scale genetic diversity with gene function for multiple species at multiple resolutions: pangenome shape, genes, sequence variants, and positions within variants. RESULTS Applied to 12,676 genomes across 12 microbial pathogenic species, we observed several shared resolution-specific patterns of genetic diversity: First, pangenome openness is associated with species' phylogenetic placement. Second, relationships between gene function and frequency are conserved across species, with core genomes enriched for metabolic and ribosomal genes and accessory genomes for trafficking, secretion, and defense-associated genes. Third, genes in core genomes with the highest sequence diversity are functionally diverse. Finally, certain protein domains are consistently mutation enriched across multiple species, especially among aminoacyl-tRNA synthetases where the extent of a domain's mutation enrichment is strongly function-dependent. CONCLUSIONS These results illustrate the value of each resolution at uncovering distinct aspects in the relationship between genetic and functional diversity across multiple species. With the continued growth of the number of sequenced genomes, these methods will reveal additional universal patterns of genetic diversity at the pangenome scale.
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Affiliation(s)
- Jason C Hyun
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA
| | - Jonathan M Monk
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
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11
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Abstract
With the advent of metagenomics, a quest began to identify the dynamics of the microbial communities in different ecological niches. Altogether, this has resulted in identification of microorganisms but is limited to only a small number of phylogenetic groups that can be easily cultured. The majority of metagenomic sequencing data remains unassigned to any known microbial group and is regarded as the "microbial dark matter." Our group is now working on integrating culturomics (isolation of pure cultures) and metagenomics from extreme environments, particularly from hot water springs and chemically contaminated soils. Our target is to culture the rare extremophiles with biotechnological significance by designing culture media based on inputs from metagenomics. While culturomics integrated with metagenomics has been extensively employed for updating the microbial catalog from the human gut, there is a need to extend this approach to extreme environmental settings to explore the microbial dark matter.
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Affiliation(s)
- Utkarsh Sood
- The Energy and Resources Institute, New Delhi, India
| | - Roshan Kumar
- Post-Graduate Department of Zoology, Magadh University, Bodh Gaya, Bihar, India
| | - Princy Hira
- Department of Zoology, Maitreyi College, University of Delhigrid.8195.5, New Delhi, India
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12
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Mongad DS, Chavan NS, Narwade NP, Dixit K, Shouche YS, Dhotre DP. MicFunPred: A conserved approach to predict functional profiles from 16S rRNA gene sequence data. Genomics 2021; 113:3635-3643. [PMID: 34450292 DOI: 10.1016/j.ygeno.2021.08.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 07/01/2021] [Accepted: 08/21/2021] [Indexed: 10/20/2022]
Abstract
The 16S rRNA gene amplicon sequencing is a popular technique that provides accurate characterization of microbial taxonomic abundances but does not provide any functional information. Several tools are available to predict functional profiles based on 16S rRNA gene sequence data that use different genome databases and approaches. As variable regions of partially-sequenced 16S rRNA gene cannot resolve taxonomy accurately beyond the genus level, these tools may give inflated results. Here, we developed 'MicFunPred', which uses a novel approach to derive imputed metagenomes based on a set of core genes only, thereby minimizing false-positive predictions. On simulated datasets, MicFunPred showed the lowest False Positive Rate (FPR) with mean Spearman's correlation of 0.89 (SD = 0.03), while on seven real datasets the mean correlation was 0.75 (SD = 0.08). MicFunPred was found to be faster with low computational requirements and performed better or comparable when compared with other tools.
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Affiliation(s)
- Dattatray S Mongad
- National Centre for Cell Science, Savitribai Phule Pune University Campus, Ganeshkhind, Pune, Maharashtra 411007, India
| | - Nikeeta S Chavan
- National Centre for Cell Science, Savitribai Phule Pune University Campus, Ganeshkhind, Pune, Maharashtra 411007, India; Persistent Systems Limited, Pune, India
| | - Nitin P Narwade
- National Centre for Cell Science, Savitribai Phule Pune University Campus, Ganeshkhind, Pune, Maharashtra 411007, India; Universidad Miguel Hernández de Elche, Alicante, Spain
| | - Kunal Dixit
- Symbiosis School of Biological Sciences (SSBS), Symbiosis International (Deemed University), Pune, Maharashtra 412115, India
| | - Yogesh S Shouche
- National Centre for Cell Science, Savitribai Phule Pune University Campus, Ganeshkhind, Pune, Maharashtra 411007, India.
| | - Dhiraj P Dhotre
- National Centre for Cell Science, Savitribai Phule Pune University Campus, Ganeshkhind, Pune, Maharashtra 411007, India.
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13
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Sharma D, Sharma A, Singh B, Verma SK. Pan-proteome profiling of emerging and re-emerging zoonotic pathogen Orientia tsutsugamushi for getting insight into microbial pathogenesis. Microb Pathog 2021; 158:105103. [PMID: 34298125 DOI: 10.1016/j.micpath.2021.105103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 07/13/2021] [Accepted: 07/16/2021] [Indexed: 01/21/2023]
Abstract
With the occurrence and evolution of antibiotic and multidrug resistance in bacteria most of the existing remedies are becoming ineffective. The pan-proteome exploration of the bacterial pathogens helps to identify the wide spectrum therapeutic targets which will be effective against all strains in a species. The current study is focused on the pan-proteome profiling of zoonotic pathogen Orientia tsutsugamushi (Ott) for the identification of potential therapeutic targets. The pan-proteome of Ott is estimated to be extensive in nature that has 1429 protein clusters, out of which 694 were core, 391 were accessory, and 344 were unique. It was revealed that 622 proteins were essential, 222 proteins were virulent factors, and 42 proteins were involved in antibiotic resistance. The potential therapeutic targets were further classified into eleven broad classes among which gene expression and regulation, transport, and metabolism were dominant. The biological interactome analysis of therapeutic targets revealed that an ample amount of interactions were present among the proteins involved in DNA replication, ribosome assembly, cellwall metabolism, cell division, and antimicrobial resistance. The predicted therapeutic targets from the pan-proteome of Ott are involved in various biological processes, virulence, and antibiotic resistance; hence envisioned as potential candidates for drug discovery to combat scrub typhus.
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Affiliation(s)
- Dixit Sharma
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Kangra, Himachal Pradesh, 176206, India.
| | - Ankita Sharma
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Kangra, Himachal Pradesh, 176206, India
| | - Birbal Singh
- ICAR-Indian Veterinary Research Institute, Regional Station, Palampur, Himachal Pradesh, 176061, India
| | - Shailender Kumar Verma
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Kangra, Himachal Pradesh, 176206, India
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14
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Evolution of Subfamily I.1 Lipases in Pseudomonas aeruginosa. Curr Microbiol 2021; 78:3494-3504. [PMID: 34279672 DOI: 10.1007/s00284-021-02589-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 06/21/2021] [Indexed: 10/20/2022]
Abstract
The gram-negative Pseudomonas aeruginosa is an opportunistic human pathogen that contains two different types of strains: the "classical" and the "outlier". In the "classical" strain, its bacterial subfamily I.1 lipases, such as LipA and LipC in P. aeruginosa PAO1, play critical roles in its pathogenicity. However, less is known about the subfamily I.1 lipases in the "outlier" strain, nor the evolution paths of those lipases in both types of P. aeruginosa strains. Our genome-scale investigation on I.1 lipases across different bacterial strains demonstrates the presence of one LipA-like and one new type of I.1 lipase (LipC2) in those "outlier" strains. The related genomic islands analyses further suggest that the LipC counterpart gene in the "outlier" strain was lost by gene truncation. In addition, the evolutionary analyses also indicates the horizontal LipC2 gene transfer from other gammaproteobacterial species, as well as the horizontal LipA gene transfer between two different phyla, both suggesting that the gene transfer of bacterial I.1 lipases might occur in different taxonomical levels. Our results not only provide an evidence to understand the pathogenicity among different P. aeruginosa strains, but add to the knowledge of I.1 lipase evolution in bacteria.
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15
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Scoffone VC, Trespidi G, Barbieri G, Irudal S, Perrin E, Buroni S. Role of RND Efflux Pumps in Drug Resistance of Cystic Fibrosis Pathogens. Antibiotics (Basel) 2021; 10:863. [PMID: 34356783 PMCID: PMC8300704 DOI: 10.3390/antibiotics10070863] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/01/2021] [Accepted: 07/13/2021] [Indexed: 01/21/2023] Open
Abstract
Drug resistance represents a great concern among people with cystic fibrosis (CF), due to the recurrent and prolonged antibiotic therapy they should often undergo. Among Multi Drug Resistance (MDR) determinants, Resistance-Nodulation-cell Division (RND) efflux pumps have been reported as the main contributors, due to their ability to extrude a wide variety of molecules out of the bacterial cell. In this review, we summarize the principal RND efflux pump families described in CF pathogens, focusing on the main Gram-negative bacterial species (Pseudomonas aeruginosa, Burkholderia cenocepacia, Achromobacter xylosoxidans, Stenotrophomonas maltophilia) for which a predominant role of RND pumps has been associated to MDR phenotypes.
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Affiliation(s)
- Viola Camilla Scoffone
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy; (V.C.S.); (G.T.); (G.B.); (S.I.)
| | - Gabriele Trespidi
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy; (V.C.S.); (G.T.); (G.B.); (S.I.)
| | - Giulia Barbieri
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy; (V.C.S.); (G.T.); (G.B.); (S.I.)
| | - Samuele Irudal
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy; (V.C.S.); (G.T.); (G.B.); (S.I.)
| | - Elena Perrin
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Silvia Buroni
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy; (V.C.S.); (G.T.); (G.B.); (S.I.)
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16
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García-Reyes S, Soto-Aceves MP, Cocotl-Yañez M, González-Valdez A, Servín-González L, Chávez GS. The outlier Pseudomonas aeruginosa strain ATCC 9027 harbors a defective LasR quorum-sensing transcriptional regulator. FEMS Microbiol Lett 2021; 367:5874253. [PMID: 32691823 DOI: 10.1093/femsle/fnaa122] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 07/17/2020] [Indexed: 12/24/2022] Open
Abstract
Pseudomonas aeruginosa infections represent an important health problem that has been recognized by the World Health Organization as a research priority. A complex regulatory network called the quorum sensing (QS) regulates several P. aeruginosa virulence-related traits, including production of elastase, rhamnolipids and pyocyanin. The avirulent P. aeruginosa strain ATCC 9027 belongs to clade 3, which is the more distant phylogroup in relationship to the other four clades of this species. This strain does not produce QS-regulated virulence factors such as elastase and rhamnolipids when cultured in rich LB medium. We report here that ATCC 9027 harbors a defective LasR protein, presumably due to the presence of an aspartic acid in position 196 instead of a glutamic acid which is the amino acid present in this position in functional LasR proteins of the type strains PAO1 (clade 1) and PA7 (also belonging to clade 3), among others. In addition, we report that ATCC 9027 and PA7 strains present differences compared to the PAO1 strain in lasB which encodes elastase, and in the rhlR regulatory sequences that modify las-boxes, and that these mutations have a little effect in the expression of these genes by a functional LasR transcriptional regulator.
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Affiliation(s)
- Selene García-Reyes
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apdo. Postal 70228, C. P. 04510, CDMX, México
| | - Martín P Soto-Aceves
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apdo. Postal 70228, C. P. 04510, CDMX, México
| | - Miguel Cocotl-Yañez
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México. C.P. 04510
| | - Abigail González-Valdez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apdo. Postal 70228, C. P. 04510, CDMX, México
| | - Luis Servín-González
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apdo. Postal 70228, C. P. 04510, CDMX, México
| | - Gloria Soberón Chávez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apdo. Postal 70228, C. P. 04510, CDMX, México
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Carbapenem Resistance Determinants Acquired through Novel Chromosomal Integrations in Extensively Drug-Resistant Pseudomonas aeruginosa. Antimicrob Agents Chemother 2021; 65:e0028921. [PMID: 33941520 PMCID: PMC8373256 DOI: 10.1128/aac.00289-21] [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] [Indexed: 12/03/2022] Open
Abstract
Two novel blaDIM-1- or blaIMP-1-containing genomic islands (GIs) were discovered by whole-genome sequence analyses in four extensively drug-resistant (XDR) Pseudomonas aeruginosa isolates from inpatients at a tertiary hospital in Ghana. The strains were of sequence type 234 (ST234) and formed a phylogenetic clade together with ST111, which is recognized as a global high-risk clone. Their carbapenem resistance was encoded by two Tn402-type integrons, In1592 (blaDIM-1) and In1595 (blaIMP-1), both carrying complete tni mobilization modules. In1595 was bound by conserved 25-bp inverted repeats (IRs) flanked by 5-bp direct repeats (DRs) associated with target site duplication. The integrons were embedded in two GIs that contained cognate integrases and were distinguished by a lower GC content than the chromosomal average. PAGI-97A (52.659 bp; In1592), which encoded a P4-type site-specific integrase of the tyrosine recombinase family in its 3′ border, was integrated into tRNA-Pro(ggg) and bracketed by a 49-bp perfect DR created by 3′-end target duplication. GIs with the same structural features, but diverse genetic content, were identified in 41/226 completed P. aeruginosa genomes. PAGI-97B (22,636 bp; In1595), which encoded an XerC/D superfamily integrase in its 5′ border, was inserted into the small RNA (sRNA) PrrF1/PrrF2 locus. Specific insertions into this highly conserved locus involved in iron-dependent regulation, all leaving PrrF1 intact, were identified in an additional six phylogenetically unrelated P. aeruginosa genomes. Our molecular analyses unveiled a hospital-associated clonal dissemination of carbapenem-resistant ST234 P. aeruginosa in which the XDR phenotype resulted from novel insertions of two GIs into specific chromosomal sites.
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18
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Fu X, Gong L, Liu Y, Lai Q, Li G, Shao Z. Bacillus pumilus Group Comparative Genomics: Toward Pangenome Features, Diversity, and Marine Environmental Adaptation. Front Microbiol 2021; 12:571212. [PMID: 34025591 PMCID: PMC8139322 DOI: 10.3389/fmicb.2021.571212] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 04/12/2021] [Indexed: 11/13/2022] Open
Abstract
Background Members of the Bacillus pumilus group (abbreviated as the Bp group) are quite diverse and ubiquitous in marine environments, but little is known about correlation with their terrestrial counterparts. In this study, 16 marine strains that we had isolated before were sequenced and comparative genome analyses were performed with a total of 52 Bp group strains. The analyses included 20 marine isolates (which included the 16 new strains) and 32 terrestrial isolates, and their evolutionary relationships, differentiation, and environmental adaptation. Results Phylogenomic analysis revealed that the marine Bp group strains were grouped into three species: B. pumilus, B. altitudinis and B. safensis. All the three share a common ancestor. However, members of B. altitudinis were observed to cluster independently, separating from the other two, thus diverging from the others. Consistent with the universal nature of genes involved in the functioning of the translational machinery, the genes related to translation were enriched in the core genome. Functional genomic analyses revealed that the marine-derived and the terrestrial strains showed differences in certain hypothetical proteins, transcriptional regulators, K+ transporter (TrK) and ABC transporters. However, species differences showed the precedence of environmental adaptation discrepancies. In each species, land specific genes were found with possible functions that likely facilitate survival in diverse terrestrial niches, while marine bacteria were enriched with genes of unknown functions and those related to transcription, phage defense, DNA recombination and repair. Conclusion Our results indicated that the Bp isolates show distinct genomic features even as they share a common core. The marine and land isolates did not evolve independently; the transition between marine and non-marine habitats might have occurred multiple times. The lineage exhibited a priority effect over the niche in driving their dispersal. Certain intra-species niche specific genes could be related to a strains adaptation to its respective marine or terrestrial environment(s). In summary, this report describes the systematic evolution of 52 Bp group strains and will facilitate future studies toward understanding their ecological role and adaptation to marine and/or terrestrial environments.
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Affiliation(s)
- Xiaoteng Fu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Linfeng Gong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Yang Liu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Guangyu Li
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
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19
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Buzzanca D, Botta C, Ferrocino I, Alessandria V, Houf K, Rantsiou K. Functional pangenome analysis reveals high virulence plasticity of Aliarcobacter butzleri and affinity to human mucus. Genomics 2021; 113:2065-2076. [PMID: 33961980 DOI: 10.1016/j.ygeno.2021.05.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 04/27/2021] [Accepted: 05/01/2021] [Indexed: 12/12/2022]
Abstract
Aliarcobacter butzleri is an emerging pathogen that may cause enteritis in humans, however, the incidence of disease caused by this member of the Campylobacteriaceae family is still underestimated. Furthermore, little is known about the precise virulence mechanism and behavior during infection. Therefore, in the present study, through complementary use of comparative genomics and physiological tests on human gut models, we sought to elucidate the genetic background of a set of 32 A. butzleri strains of diverse origin and to explore the correlation with the ability to colonize and invade human intestinal cells in vitro. The simulated infection of human intestinal models showed a higher colonization rate in presence of mucus-producing cells. For some strains, human mucus significantly improved the resistance to physical removal from the in vitro mucosa, while short time-frame growth was even observed. Pangenome analysis highlighted a hypervariable accessory genome, not strictly correlated to the isolation source. Likewise, the strain phylogeny was unrelated to their shared origin, despite a certain degree of segregation was observed among strains isolated from different segments of the intestinal tract of pigs. The putative virulence genes detected in all strains were mostly encompassed in the accessory fraction of the pangenome. The LPS biosynthesis and in particular the chain glycosylation of the O-antigen is harbored in a region of high plasticity of the pangenome, which would indicate frequent horizontal gene transfer phenomena, as well as the involvement of this hypervariable structure in the adaptive behavior and sympatric evolution of A. butzleri. Results of the present study deepen the current knowledge on A. butzleri pangenome by extending the pool of genes regarded as virulence markers and provide bases to develop new diagnostic approaches for the detection of those strains with a higher virulence potential.
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Affiliation(s)
- Davide Buzzanca
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Turin, Italy; Department of Veterinary Public Health, Faculty of Veterinary Medicine, Ghent University, Belgium
| | - Cristian Botta
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Turin, Italy
| | - Ilario Ferrocino
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Turin, Italy
| | - Valentina Alessandria
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Turin, Italy
| | - Kurt Houf
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Ghent University, Belgium
| | - Kalliopi Rantsiou
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Turin, Italy.
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20
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Singh P, Hira P, Rawat CD, Lal R, Sood U. Genome-based reclassification of Amycolatopsis eurytherma as a later heterotypic synonym of Amycolatopsis thermoflava. Int J Syst Evol Microbiol 2021; 71. [PMID: 33470925 DOI: 10.1099/ijsem.0.004642] [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] [Indexed: 12/15/2022] Open
Abstract
The present study was carried out to clarify the taxonomic assignment of two closely related Amycolatopsis species. Genomic information for 48 type strains was available at the time of conducting this analysis. Our analysis showed that two species, viz. Amycolatopsis eurytherma Kim et al. 2002 and Amycolatopsis thermoflava Chun et al. 1999, are conspecific. The 16S rRNA gene sequences of the two species possess 98.85 % sequence similarity. Further, whole-genome comparisons showed that A. eurytherma DSM 44348T and A. thermoflava N1165T shared 98.75 % average nucleotide identity, 98.63 % average amino acid identity and 87.8 % digital DNA-DNA hybridization values. These values exceed the threshold values for bacterial species delineation, indicating that they belong to the same species. Further, the phylogenomic analysis based on the core genome of the strains under study confirmed that A. eurytherma DSM 44348T and A. thermoflava N1165T formed a monophyletic clade. Based on this evidence we propose the reclassification of Amycolatopsis eurytherma Kim et al. 2002 as a later heterotypic synonym of Amycolatopsis thermoflava Chun et al. 1999.
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Affiliation(s)
- Priya Singh
- Department of Zoology, Acharya Narendra Dev College, University of Delhi, New Delhi-110019, India
| | - Princy Hira
- Department of Zoology, Maitreyi College, University of Delhi, New Delhi-110021, India
| | - Charu Dogra Rawat
- Molecular Biology and Genomics Research Laboratory, Ramjas College, University of Delhi, Delhi-110007, India
| | - Rup Lal
- The Energy and Resources Institute, Lodhi Road, New Delhi-110003, India
| | - Utkarsh Sood
- The Energy and Resources Institute, Lodhi Road, New Delhi-110003, India
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21
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Wang X, Li D, Gao P, Gu W, He X, Yang W, Tang W. Analysis of biosorption and biotransformation mechanism of Pseudomonas chengduensis strain MBR under Cd(II) stress from genomic perspective. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 198:110655. [PMID: 32361136 DOI: 10.1016/j.ecoenv.2020.110655] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 04/15/2020] [Accepted: 04/17/2020] [Indexed: 06/11/2023]
Abstract
Microbial treatment of heavy metal-polluted sites is considered an environmentally friendly bioremediation technology with high potential. This study shows that Pseudomonas chengduensis strain MBR, a bacterium that can potentially be applied in the treatment of heavy metal pollution, is most affected by Cd(II) stress at the beginning of its growth. Up to 100% of total Cd(II) adsorption occurs in the first 48 h after treatment of stationary phase cells with Cd(II). A biofilm forms on the cell surface, Cd(II) adsorbs, and is reduced to Cd (0) in the form of nanoscale particles. The genome of strain MBR was sequenced, annotated and analyzed. We identified various genes potentially related to cadmium resistance, transport and metabolism. Analysis of the strain MBR genome is helpful to explore the mechanism of Cd(II) resistance, and can provide new ideas for cadmium pollution control.
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Affiliation(s)
- Xu Wang
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu, 610041, China; College of Life Sciences, Sichuan University, Chengdu, 610064, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Daping Li
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu, 610041, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Ping Gao
- College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Wenzhi Gu
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu, 610041, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaohong He
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu, 610041, China
| | - Wenyi Yang
- College of Environmental Sciences, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wenzhong Tang
- State Key Laboratory on Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 10085, China
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22
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Current status of pan-genome analysis for pathogenic bacteria. Curr Opin Biotechnol 2020; 63:54-62. [DOI: 10.1016/j.copbio.2019.12.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 11/16/2019] [Accepted: 12/02/2019] [Indexed: 02/07/2023]
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23
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de Sales RO, Migliorini LB, Puga R, Kocsis B, Severino P. A Core Genome Multilocus Sequence Typing Scheme for Pseudomonas aeruginosa. Front Microbiol 2020; 11:1049. [PMID: 32528447 PMCID: PMC7264379 DOI: 10.3389/fmicb.2020.01049] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 04/28/2020] [Indexed: 12/15/2022] Open
Abstract
Pseudomonas aeruginosa is a ubiquitous microorganism and an important opportunistic pathogen responsible for a broad spectrum of infections mainly in immunosuppressed and critically ill patients. Molecular investigations traditionally rely on pulsed field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). In this work we propose a core genome multilocus sequence typing (cgMLST) scheme for P. aeruginosa, a methodology that combines traditional MLST principles with whole genome sequencing data. All publicly available complete P. aeruginosa genomes, representing the diversity of this species, were used to establish a cgMLST scheme targeting 2,653 genes. The scheme was then tested using genomes available at contig, chromosome and scaffold levels. The proposed cgMLST scheme for P. aeruginosa typed over 99% (2,314/2,325) of the genomes available for this study considering at least 95% of the cgMLST target genes present. The absence of a certain number gene targets at the threshold considered for both the creation and validation steps due to low genome sequence quality is possibly the main reason for this result. The cgMLST scheme was compared with previously published whole genome single nucleotide polymorphism analysis for the characterization of the population structure of the epidemic clone ST235 and results were highly similar. In order to evaluate the typing resolution of the proposed scheme, collections of isolates belonging to two important STs associated with cystic fibrosis, ST146 and ST274, were typed using this scheme, and ST235 isolates associated with an outbreak were evaluated. Besides confirming the relatedness of all the isolates, earlier determined by MLST, the higher resolution of cgMLST denotes that it may be suitable for surveillance programs, overcoming possible shortcomings of classical MLST. The proposed scheme is publicly available at: https://github.com/BioinformaticsHIAEMolecularMicrobiology/cgMLST-Pseudomonas-aeruginosa.
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Affiliation(s)
- Romário Oliveira de Sales
- Hospital Israelita Albert Einstein, Albert Einstein Research and Education Institute, São Paulo, Brazil
| | - Letícia Busato Migliorini
- Hospital Israelita Albert Einstein, Albert Einstein Research and Education Institute, São Paulo, Brazil
| | - Renato Puga
- Hospital Israelita Albert Einstein, Albert Einstein Research and Education Institute, São Paulo, Brazil
| | - Bela Kocsis
- Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary
| | - Patricia Severino
- Hospital Israelita Albert Einstein, Albert Einstein Research and Education Institute, São Paulo, Brazil
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24
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Singhvi N, Gupta V, Singh P, Prakash O, Bechthold A, Singh Y, Lal R. Prediction of Transcription Factors and Their Involvement in Regulating Rifamycin Production in Amycolatopsis mediterranei S699. Indian J Microbiol 2020; 60:310-317. [PMID: 32655198 DOI: 10.1007/s12088-020-00868-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 04/03/2020] [Indexed: 12/16/2022] Open
Abstract
Amycolatopsis mediterranei S699 produces rifamycin B and successors of this strain are in use for the industrial production of rifamycin B. Semisynthetic derivatives of rifamycin B are used against Mycobacterium tuberculosis that causes tuberculosis. Although the rifamycin biosynthetic gene cluster was characterized two decades ago, the regulation of rifamycin B biosynthesis in Amycolatopsis mediterranei S699 is poorly understood. In this study, we analysed the genome and proteome of Amycolatopsis mediterranei S699 and identified 1102 transcription factors which comprise about 10% of the total genome. Using interactomics approaches we delineated 30 unique transcription factors directly involved in secondary metabolism that regulate rifamycin B biosynthesis. We also predict the role of RifN as hub in controlling the regulation of other genes involved in rifamycin biosynthesis. RifN is important for maintaining the integrity of the rifamycin-network. Thus, these transcription factor can be exploited to improve rifamycin B production in Amycolatopsis mediterranei S699.
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Affiliation(s)
- Nirjara Singhvi
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Vipin Gupta
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Priya Singh
- Department of Zoology, University of Delhi, Delhi, 110007 India.,Present Address: Acharya Narendra Dev College, University of Delhi, New Delhi, 110019 India
| | - Om Prakash
- National Centre for Cell Sciences, Pune, Maharashtra 411007 India
| | - Andreas Bechthold
- Pharmaceutical Biology and Biotechnology, Institute of Pharmaceutical Sciences, Albert-Ludwigs University, 79104 Freiburg, Germany
| | - Yogendra Singh
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Rup Lal
- The Energy and Resources Institute, Darbari Seth Block, IHC Complex, New Delhi, 110033 India
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25
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Trouillon J, Sentausa E, Ragno M, Robert-Genthon M, Lory S, Attrée I, Elsen S. Species-specific recruitment of transcription factors dictates toxin expression. Nucleic Acids Res 2020; 48:2388-2400. [PMID: 31925438 PMCID: PMC7049718 DOI: 10.1093/nar/gkz1232] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 12/17/2019] [Accepted: 12/21/2019] [Indexed: 12/13/2022] Open
Abstract
Tight and coordinate regulation of virulence determinants is essential for bacterial biology and involves dynamic shaping of transcriptional regulatory networks during evolution. The horizontally transferred two-partner secretion system ExlB-ExlA is instrumental in the virulence of different Pseudomonas species, ranging from soil- and plant-dwelling biocontrol agents to the major human pathogen Pseudomonas aeruginosa. Here, we identify a Cro/CI-like repressor, named ErfA, which together with Vfr, a CRP-like activator, controls exlBA expression in P. aeruginosa. The characterization of ErfA regulon across P. aeruginosa subfamilies revealed a second conserved target, the ergAB operon, with functions unrelated to virulence. To gain insights into this functional dichotomy, we defined the pan-regulon of ErfA in several Pseudomonas species and found ergAB as the sole conserved target of ErfA. The analysis of 446 exlBA promoter sequences from all exlBA+ genomes revealed a wide variety of regulatory sequences, as ErfA- and Vfr-binding sites were found to have evolved specifically in P. aeruginosa and nearly each species carries different regulatory sequences for this operon. We propose that the emergence of different regulatory cis-elements in the promoters of horizontally transferred genes is an example of plasticity of regulatory networks evolving to provide an adapted response in each individual niche.
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Affiliation(s)
- Julian Trouillon
- Université Grenoble Alpes, CNRS ERL5261, CEA-IRIG-BCI, INSERM UMR1036, Grenoble 38000, France
| | - Erwin Sentausa
- Université Grenoble Alpes, CNRS ERL5261, CEA-IRIG-BCI, INSERM UMR1036, Grenoble 38000, France
| | - Michel Ragno
- Université Grenoble Alpes, CNRS ERL5261, CEA-IRIG-BCI, INSERM UMR1036, Grenoble 38000, France
| | - Mylène Robert-Genthon
- Université Grenoble Alpes, CNRS ERL5261, CEA-IRIG-BCI, INSERM UMR1036, Grenoble 38000, France
| | - Stephen Lory
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Ina Attrée
- Université Grenoble Alpes, CNRS ERL5261, CEA-IRIG-BCI, INSERM UMR1036, Grenoble 38000, France
| | - Sylvie Elsen
- Université Grenoble Alpes, CNRS ERL5261, CEA-IRIG-BCI, INSERM UMR1036, Grenoble 38000, France
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26
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Sood U, Singh DN, Hira P, Lee JK, Kalia VC, Lal R, Shakarad M. Rapid and solitary production of mono-rhamnolipid biosurfactant and biofilm inhibiting pyocyanin by a taxonomic outlier Pseudomonas aeruginosa strain CR1. J Biotechnol 2020; 307:98-106. [DOI: 10.1016/j.jbiotec.2019.11.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 10/15/2019] [Accepted: 11/04/2019] [Indexed: 01/20/2023]
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27
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Hira P, Singh P, Pinnaka AK, Korpole S, Lal R. Taxonomically Characterized and Validated Bacterial Species Based on 16S rRNA Gene Sequences from India During the Last Decade. Indian J Microbiol 2019; 60:54-61. [PMID: 32089574 DOI: 10.1007/s12088-019-00845-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 11/27/2019] [Indexed: 12/26/2022] Open
Abstract
Microbial taxonomy dealing with identification and characterization of prokaryotes like bacteria and archaea has always been a major area of research all over the world. Exploring diversity of microbes and description of novel species with different genes and secondary compounds is of utmost importance for better future and sustenance of life. India having an enormous range of ecosystems and diverse species inhabiting these niches is considered to be one of the richest biodiversity regions of the world. During the last decade, with newer methodologies and better technology, the prokaryotic taxonomy from India has extended our inventory of microbial communities in specific niches. However, there still exist some limitations in classifying the microbes from India as compared to that is done world-over. This review enlists the taxonomic description of novel taxa of prokaryotes from India in the past decade. A total of 378 new bacterial species have been classified from different habitats in India in the last ten years and no descriptions of archaeal species is documented till date.
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Affiliation(s)
- Princy Hira
- 1Department of Zoology, Maitreyi College (University of Delhi), Chanakyapuri, New Delhi 110021 India
| | - Priya Singh
- 2Department of Zoology, Acharya Narendra Dev College (University of Delhi), Govindpuri, Kalkaji, New Delhi, 110019 India
| | - Anil Kumar Pinnaka
- 3CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036 India
| | - Suresh Korpole
- 3CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036 India
| | - Rup Lal
- The Energy and Resource Institute, Darbari Seth Block, IHC Complex, Lodhi Road, New Delhi, 110003 India
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28
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Singh DN, Sood U, Singh AK, Gupta V, Shakarad M, Rawat CD, Lal R. Genome Sequencing Revealed the Biotechnological Potential of an Obligate Thermophile Geobacillus thermoleovorans Strain RL Isolated from Hot Water Spring. Indian J Microbiol 2019; 59:351-355. [PMID: 31388213 DOI: 10.1007/s12088-019-00809-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 06/04/2019] [Indexed: 01/11/2023] Open
Abstract
In the present study, we report the draft genome sequence of an obligate thermophile Geobacillus thermoleovorans strain RL isolated from Manikaran hot water spring located atop the Himalayan ranges, India. Strain RL grew optimally at 70 °C but not below 45 °C. The draft genome (3.39 Mb) obtained by Illumina sequencing contains 138 contigs with an average G + C content of 52.30%. RAST annotation showed that amino acid metabolism pathways were most dominant followed by carbohydrate metabolism. Genome-wide analysis using NCBI's Prokaryotic Genome Annotation Pipeline revealed that strain RL encodes for a cocktail of industrially important hydrolytic enzymes glycoside hydrolase, α-and β-glucosidase, xylanase, amylase, neopullulanase, pullulanase and lipases required for white biotechnology. In addition, the presence of genes encoding green biocatalyst multicopper polyphenol oxidase (laccase) and an anticancer enzyme l-glutaminase reflects the significance of strain RL in gray and red biotechnology, respectively. Strain RL is a thermophilic multi-enzyme encoding bacterium which could be the source for the recombinant production of biotechnologically significant enzymes. In, addition whole cells of strain RL may be used in bioremediation studies.
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Affiliation(s)
| | - Utkarsh Sood
- 1Department of Zoology, University of Delhi, Delhi, 110007 India.,Present Address: PhiXGen Private Limited, Gurugram, Haryana 122001 India
| | - Amit Kumar Singh
- 3Department of Biotechnology, Jamia Millia Islamia, New Delhi, Delhi 110025 India
| | - Vipin Gupta
- 1Department of Zoology, University of Delhi, Delhi, 110007 India.,Present Address: PhiXGen Private Limited, Gurugram, Haryana 122001 India
| | | | - Charu Dogra Rawat
- 4Department of Zoology, Ramjas College, University of Delhi, Delhi, 110007 India
| | - Rup Lal
- 1Department of Zoology, University of Delhi, Delhi, 110007 India.,Present Address: PhiXGen Private Limited, Gurugram, Haryana 122001 India
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