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Dulya O, Mikryukov V, Shchepkin DV, Pent M, Tamm H, Guazzini M, Panagos P, Jones A, Orgiazzi A, Marroni F, Bahram M, Tedersoo L. A trait-based ecological perspective on the soil microbial antibiotic-related genetic machinery. ENVIRONMENT INTERNATIONAL 2024; 190:108917. [PMID: 39089094 DOI: 10.1016/j.envint.2024.108917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/24/2024] [Accepted: 07/25/2024] [Indexed: 08/03/2024]
Abstract
Antibiotic resistance crisis dictates the need for resistance monitoring and the search for new antibiotics. The development of monitoring protocols is hindered by the great diversity of resistance factors, while the "streetlight effect" denies the possibility of discovering novel drugs based on existing databases. In this study, we address these challenges using high-throughput environmental screening viewed from a trait-based ecological perspective. Through an in-depth analysis of the metagenomes of 658 topsoil samples spanning Europe, we explored the distribution of 241 prokaryotic and fungal genes responsible for producing metabolites with antibiotic properties and 485 antibiotic resistance genes. We analyzed the diversity of these gene collections at different levels and modeled the distribution of each gene across environmental gradients. Our analyses revealed several nonparallel distribution patterns of the genes encoding sequential steps of enzymatic pathways synthesizing large antibiotic groups, pointing to gaps in existing databases and suggesting potential for discovering new analogues of known antibiotics. We show that agricultural activity caused a continental-scale homogenization of microbial antibiotic-related machinery, emphasizing the importance of maintaining indigenous ecosystems within the landscape mosaic. Based on the relationships between the proportion of the genes in the metagenomes with the main predictors (soil pH, land cover type, climate temperature and humidity), we illustrate how the properties of chemical structures dictate the distribution of the genes responsible for their synthesis across environments. With this understanding, we propose general principles to facilitate the discovery of antibiotics, including principally new ones, establish abundance baselines for antibiotic resistance genes, and predict their dissemination.
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Affiliation(s)
- Olesya Dulya
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu 50409, Estonia; Center of Mycology and Microbiology, University of Tartu, Tartu 50409, Estonia.
| | - Vladimir Mikryukov
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu 50409, Estonia; Center of Mycology and Microbiology, University of Tartu, Tartu 50409, Estonia.
| | - Daniil V Shchepkin
- Center of Mycology and Microbiology, University of Tartu, Tartu 50409, Estonia.
| | - Mari Pent
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu 50409, Estonia.
| | - Heidi Tamm
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu 50409, Estonia.
| | - Massimo Guazzini
- Department of Agriculture, Food, Environmental and Animal Sciences, University of Udine, Udine 33100, Italy.
| | - Panos Panagos
- European Commission, Joint Research Centre (JRC), Ispra, Province of Varese 21027, Italy.
| | - Arwyn Jones
- European Commission, Joint Research Centre (JRC), Ispra, Province of Varese 21027, Italy.
| | - Alberto Orgiazzi
- European Commission, Joint Research Centre (JRC), Ispra, Province of Varese 21027, Italy; European Dynamics, Brussels B-1000, Belgium.
| | - Fabio Marroni
- Department of Agriculture, Food, Environmental and Animal Sciences, University of Udine, Udine 33100, Italy.
| | - Mohammad Bahram
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu 50409, Estonia; Department of Ecology, Swedish University of Agricultural Sciences, Uppsala 75007, Sweden; Department of Agroecology, Aarhus University, Forsøgsvej 1 4200, Slagelse, Denmark.
| | - Leho Tedersoo
- Center of Mycology and Microbiology, University of Tartu, Tartu 50409, Estonia.
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Nag N, Ray T, Tapader R, Gope A, Das R, Mahapatra E, Saha S, Pal A, Prasad P, Pal A. Metallo-protease Peptidase M84 from Bacillusaltitudinis induces ROS-dependent apoptosis in ovarian cancer cells by targeting PAR-1. iScience 2024; 27:109828. [PMID: 38799586 PMCID: PMC11126781 DOI: 10.1016/j.isci.2024.109828] [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: 10/05/2023] [Revised: 01/02/2024] [Accepted: 04/24/2024] [Indexed: 05/29/2024] Open
Abstract
We have purified Peptidase M84 from Bacillus altitudinis in an effort to isolate anticancer proteases from environmental microbial isolates. This metallo-protease had no discernible impact on normal cell survival, but it specifically induced apoptosis in ovarian cancer cells. PAR-1, a GPCR which is reported to be overexpressed in ovarian cancer cells, was identified as a target of Peptidase M84. We observed that Peptidase M84 induced PAR-1 overexpression along with activating its downstream signaling effectors NF-κB and MAPK to promote excessive reactive oxygen species (ROS) generation. This evoked apoptotic death of the ovarian cancer cells through the intrinsic route. In in vivo set-up, weekly intraperitoneal administration of Peptidase M84 in syngeneic mice significantly diminished ascites accumulation, increasing murine survival rates by 60%. Collectively, our findings suggested that Peptidase M84 triggered PAR-1-mediated oxidative stress to act as an apoptosis inducer. This established Peptidase M84 as a drug candidate for receptor mediated targeted-therapy of ovarian cancer.
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Affiliation(s)
- Niraj Nag
- Division of Molecular Pathophysiology, ICMR-National Institute of Cholera and Enteric Diseases (ICMR-NICED), P-33, CIT Road, Scheme-XM, Beliaghata, Kolkata, West Bengal 700010, India
| | - Tanusree Ray
- Division of Molecular Pathophysiology, ICMR-National Institute of Cholera and Enteric Diseases (ICMR-NICED), P-33, CIT Road, Scheme-XM, Beliaghata, Kolkata, West Bengal 700010, India
| | - Rima Tapader
- Division of Molecular Pathophysiology, ICMR-National Institute of Cholera and Enteric Diseases (ICMR-NICED), P-33, CIT Road, Scheme-XM, Beliaghata, Kolkata, West Bengal 700010, India
| | - Animesh Gope
- Division of Clinical Medicine, ICMR-National Institute of Cholera and Enteric Diseases (ICMR-NICED), P-33, CIT Road, Scheme-XM, Beliaghata, Kolkata, West Bengal 700010, India
| | - Rajdeep Das
- Molecular Cell Biology of Autophagy Lab, The Francis Crick Institute, 1, Midland Road, London NW1 1AT, UK
| | - Elizabeth Mahapatra
- Department of Environmental Carcinogenesis and Toxicology, Chittaranjan National Cancer Institute, 37, S.P. Mukherjee Road, Kolkata, West Bengal 700026, India
| | - Saibal Saha
- Division of Molecular Pathophysiology, ICMR-National Institute of Cholera and Enteric Diseases (ICMR-NICED), P-33, CIT Road, Scheme-XM, Beliaghata, Kolkata, West Bengal 700010, India
| | - Ananda Pal
- Division of Clinical Medicine, ICMR-National Institute of Cholera and Enteric Diseases (ICMR-NICED), P-33, CIT Road, Scheme-XM, Beliaghata, Kolkata, West Bengal 700010, India
| | - Parash Prasad
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital and Medical Center, 3333 Burnet Avenue, Cincinnati 45229-3026, OH, USA
| | - Amit Pal
- Division of Molecular Pathophysiology, ICMR-National Institute of Cholera and Enteric Diseases (ICMR-NICED), P-33, CIT Road, Scheme-XM, Beliaghata, Kolkata, West Bengal 700010, India
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3
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Kulkarni BS, Makde RD, Jamdar SN. Characterization of a secreted aminopeptidase of M28 family from B. fragilis and its possible role in protein metabolism in the gut. Biochim Biophys Acta Gen Subj 2024; 1868:130598. [PMID: 38499114 DOI: 10.1016/j.bbagen.2024.130598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 03/09/2024] [Accepted: 03/13/2024] [Indexed: 03/20/2024]
Abstract
Products of microbial protein metabolism in the gut can influence the health of the host in many ways. Members of the Bacteriodales, major commensals of the human colon have been associated with long-term intake of high-protein diets. Undigested proteins or peptides that reach the colon can be hydrolyzed by extra-cellular proteases found in some Bacteroides species into amino acids and peptides which can be further catabolized. In this communication, we have characterized one such secreted aminopeptidase (BfAP) from Bacteroides fragilis belonging to the M28 family which is capable of degrading peptides released from soybean protein after predigestion in the small intestine. The BfAP enzyme was cloned, expressed in E. coli, and purified to homogeneity. It is a metallopeptidase requiring Co2+ ion for optimum activity at 55 °C and pH 8 and preferentially cleaves neutral aliphatic (Met/Leu) and positively charged (Arg/Lys) amino acids from the N-terminus of peptides. It showed high specificity for long peptides as well as proteins like β-casein. Structural analysis of BfAP and its orthologues using AlphaFold2 reveal a shared highly conserved M28 domain, but vary with respect to their N-terminal region with some of them possessing an additional cap domain which may be important for regulation of substrate binding. Although BfAP lacks the typical cap domain, it shows small extensions that can form a loop adjacent to the proposed active site and may affect substrate binding. We suggest that this secreted enzyme may play an important role in protein metabolism in the colon where Bacteroides species are abundant.
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Affiliation(s)
- Bhushan S Kulkarni
- Food Technology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Life Sciences Department, Homi Bhabha National Institute, Mumbai 400094, India
| | - Ravindra D Makde
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai 400085, India; Life Sciences Department, Homi Bhabha National Institute, Mumbai 400094, India
| | - Sahayog N Jamdar
- Food Technology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Life Sciences Department, Homi Bhabha National Institute, Mumbai 400094, India.
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Ekpenyong M, Asitok A, Ben U, Amenaghawon A, Kusuma H, Akpan A, Antai S. Application of the novel manta-ray foraging algorithm to optimize acidic peptidase production in solid-state fermentation using binary agro-industrial waste. Prep Biochem Biotechnol 2024; 54:226-238. [PMID: 37210635 DOI: 10.1080/10826068.2023.2214936] [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: 05/22/2023]
Abstract
Peptidases, which constitute about 20% of the global enzyme market, have found applications in detergent, food and pharmaceutical industries, and could be produced on a large scale using low-cost agro-industrial waste. An acidophilic Bacillus cereus strain produced acidic peptidase on binary-agro-industrial waste comprising yam peels and fish processing waste at pH 4.5 with high catalytic activity. A five-variable central composite rotatable design of a response surface methodology was used to model bioprocess conditions for improved peptidase production in solid-state fermentation. Data generated was leveraged as the basis for applying the novel Manta-ray foraging optimization-linked feed-forward artificial neural network to predict bioprocess conditions optimally. Results obtained from the optimization experiments revealed a significant coefficient of determination of 0.9885 with low-performance error. The bioprocess predicted a peptidase activity of 1035.32 U/mL under optimized conditions set as 54.8 g/100 g yam peels, 23.85 g/100 g fish waste, 0.31 g/100 g CaCl2, 47.54% (v/w) moisture content, and pH 2. Peptidase activity was improved 5-fold, and was stable for 240 min between pH 2.5 and 3.5. Michaelis-Menten kinetics revealed a Km of 0.119 mM and a catalytic efficiency of 45462.19 mM-1 min-1. The bioprocess holds promise for sustainable enzyme-driven applications.
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Affiliation(s)
- Maurice Ekpenyong
- Environmental Microbiology and Biotechnology Unit, Department of Microbiology, Faculty of Biological Sciences, University of Calabar, Calabar, Nigeria
- University of Calabar Collection of Microorganisms (UCCM), University of Calabar, Calabar, Nigeria
| | - Atim Asitok
- Environmental Microbiology and Biotechnology Unit, Department of Microbiology, Faculty of Biological Sciences, University of Calabar, Calabar, Nigeria
- University of Calabar Collection of Microorganisms (UCCM), University of Calabar, Calabar, Nigeria
| | - Ubong Ben
- Department of Physics, Faculty of Physical Sciences, University of Calabar, Calabar, Nigeria
| | - Andrew Amenaghawon
- Department of Chemical Engineering, Faculty of Engineering, University of Benin, Benin-City, Nigeria
| | - Heri Kusuma
- Department of Chemical Engineering, Faculty of Industrial Technology, Universitas Pembangunan Nasional "Veteran" Yogyakarta, Yogyakarta, Indonesia
| | - Anthony Akpan
- Department of Physics, Faculty of Physical Sciences, University of Calabar, Calabar, Nigeria
| | - Sylvester Antai
- Environmental Microbiology and Biotechnology Unit, Department of Microbiology, Faculty of Biological Sciences, University of Calabar, Calabar, Nigeria
- University of Calabar Collection of Microorganisms (UCCM), University of Calabar, Calabar, Nigeria
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5
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Sieradzki ET, Nuccio EE, Pett-Ridge J, Firestone MK. Rhizosphere and detritusphere habitats modulate expression of soil N-cycling genes during plant development. mSystems 2023; 8:e0031523. [PMID: 37754554 PMCID: PMC10654102 DOI: 10.1128/msystems.00315-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 08/07/2023] [Indexed: 09/28/2023] Open
Abstract
IMPORTANCE Plant roots modulate microbial nitrogen (N) cycling by regulating the supply of root-derived carbon and nitrogen uptake. These differences in resource availability cause distinct micro-habitats to develop: soil near living roots, decaying roots, near both, or outside the direct influence of roots. While many environmental factors and genes control the microbial processes involved in the nitrogen cycle, most research has focused on single genes and pathways, neglecting the interactive effects these pathways have on each other. The processes controlled by these pathways determine consumption and production of N by soil microorganisms. We followed the expression of N-cycling genes in four soil microhabitats over a period of active root growth for an annual grass. We found that the presence of root litter and living roots significantly altered gene expression involved in multiple nitrogen pathways, as well as tradeoffs between pathways, which ultimately regulate N availability to plants.
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Affiliation(s)
- Ella T. Sieradzki
- Department of Environmental Science, Policy and Management, University of California Berkeley, Berkeley, California, USA
| | - Erin E. Nuccio
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
- Life & Environmental Sciences Department, UC Merced, Merced, California, USA
- Innovative Genomics Institute, UC Berkeley, Berkeley, California, USA
| | - Mary K. Firestone
- Department of Environmental Science, Policy and Management, University of California Berkeley, Berkeley, California, USA
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Nwankwo C, Hou J, Cui HL. Extracellular proteases from halophiles: diversity and application challenges. Appl Microbiol Biotechnol 2023; 107:5923-5934. [PMID: 37566160 DOI: 10.1007/s00253-023-12721-y] [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: 05/29/2023] [Revised: 07/26/2023] [Accepted: 08/01/2023] [Indexed: 08/12/2023]
Abstract
Halophilic extracellular proteases offer promising application in various fields. Information on these prominent proteins including the synthesizing organisms, biochemical properties, domain organisation, purification, and application challenges has never been covered in recent reviews. Although extracellular proteases from bacteria pioneered the study of proteases in halophiles, progress is being made in proteases from halophilic archaea. Recent advances in extracellular proteases from archaea revealed that archaeal proteases are more robust and applicable. Extracellular proteases are composed of domains that determine their mechanisms of action. The intriguing domain structure of halophilic extracellular proteases consists of N-terminal domain, catalytic domain, and C-terminal extension. The role of C-terminal domains varies among different organisms. A high diversity of C-terminal domains would endow the proteases with diverse functions. With the development of genomics, culture-independent methods involving heterologous expression, affinity chromatography, and in vitro refolding are deployed with few challenges on purification and presenting novel research opportunities. Halophilic extracellular proteases have demonstrated remarkable potentials in industries such as detergent, leather, peptide synthesis, and biodegradation, with desirable properties and ability to withstand harsh industrial processes. KEY POINTS: • Halophilic extracellular proteases have robust properties suitable for applications. • A high diversity of C-terminal domains may endow proteases with diverse properties. • Novel protease extraction methods present novel application opportunities.
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Affiliation(s)
- Chidiebele Nwankwo
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, 212013, Jiangsu, People's Republic of China
- Natural Sciences Unit, School of General Studies, University of Nigeria, Nsukka, 410002, Enugu State, Nigeria
- Department of Microbiology, Faculty of Biological Sciences, University of Nigeria, Nsukka, 410002, Enugu State, Nigeria
| | - Jing Hou
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, 212013, Jiangsu, People's Republic of China.
| | - Heng-Lin Cui
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, 212013, Jiangsu, People's Republic of China.
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Kim J, Cha IT, Lee KE, Son YK, Yu J, Seol D. Genomic insights and comparative analysis of Flavobacterium bizetiae HJ-32-4 isolated from soil. Antonie Van Leeuwenhoek 2023; 116:975-986. [PMID: 37542623 DOI: 10.1007/s10482-023-01858-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 07/19/2023] [Indexed: 08/07/2023]
Abstract
In the late 1970s, Flavobacterium bizetiae was first isolated from diseased fish in Canada. After four decades of preservation, it was reported as a novel species in 2020. Here, we report the first complete genome sequence of HJ-32-4, a novel strain of F. bizetiae. Interestingly, HJ-32-4 was isolated from soil in Gangwon-do, Republic of Korea, unlike the other two previously reported F. bizetiae strains which were isolated from fish. We generated a single circular chromosome of HJ-32-4, comprising 5,745,280 bp with a GC content of 34.2%. The average nucleotide identity (ANI) value of 96.2% indicated that HJ-32-4 belongs to F. bizetiae CIP 105534T. The virulence factor was not detected in the genome. Comparative genomic analysis of F. bizetiae and major flavobacterial pathogens revealed that F. bizetiae had a larger genome size and the ratio of peptidases (PEP) and glycoside hydrolase (GH) genes of F. bizetiae were lower than those of the rest strains, implying that F. bizetiae exhibits similar characteristics with non-pathogenic strains from a genomic point of view. However, further experimental verification is required to ensure these in silico predictions. This study will provide insight into the overall characteristics of HJ-32-4 compared to other strains.
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Affiliation(s)
- Jisu Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - In-Tae Cha
- National Institute of Biological Resources, 42 Hwangyeong-ro, Seo-gu, Incheon, 22689, Republic of Korea
| | - Ki-Eun Lee
- National Institute of Biological Resources, 42 Hwangyeong-ro, Seo-gu, Incheon, 22689, Republic of Korea
| | - Youn Kyoung Son
- National Institute of Biological Resources, 42 Hwangyeong-ro, Seo-gu, Incheon, 22689, Republic of Korea
| | - Jaewoong Yu
- eGnome, Inc., 26 Beobwon-ro 9-gil, Songpa-gu, Seoul, 05836, Republic of Korea.
| | - Donghyeok Seol
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.
- Department of Surgery, Seoul National University Bundang Hospital, 172 Dolma-ro, Bundang-gu, Seongnam, 13605, Republic of Korea.
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Rigo GV, Cardoso FG, Pereira MM, Devereux M, McCann M, Santos ALS, Tasca T. Peptidases Are Potential Targets of Copper(II)-1,10-Phenanthroline-5,6-dione Complex, a Promising and Potent New Drug against Trichomonas vaginalis. Pathogens 2023; 12:pathogens12050745. [PMID: 37242415 DOI: 10.3390/pathogens12050745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/09/2023] [Accepted: 05/17/2023] [Indexed: 05/28/2023] Open
Abstract
Trichomonas vaginalis is responsible for 156 million new cases per year worldwide. When present asymptomatically, the parasite can lead to serious complications, such as development of cervical and prostate cancer. As infection increases the acquisition and transmission of HIV, the control of trichomoniasis represents an important niche for the discovery and development of new antiparasitic molecules. This urogenital parasite synthesizes several molecules that allow the establishment and pathogenesis of infection. Among them, peptidases occupy key roles as virulence factors, and the inhibition of these enzymes has become an important mechanism for modulating pathogenesis. Based on these premises, our group recently reported the potent anti-T. vaginalis action of the metal-based complex [Cu(phendione)3](ClO4)2.4H2O (Cu-phendione). In the present study, we evaluated the influence of Cu-phendione on the modulation of proteolytic activities produced by T. vaginalis by biochemical and molecular approaches. Cu-phendione showed strong inhibitory potential against T. vaginalis peptidases, especially cysteine- and metallo-type peptidases. The latter revealed a more prominent effect at both the post-transcriptional and post-translational levels. Molecular Docking analysis confirmed the interaction of Cu-phendione, with high binding energy (-9.7 and -10.7 kcal·mol-1, respectively) at the active site of both TvMP50 and TvGP63 metallopeptidases. In addition, Cu-phendione significantly reduced trophozoite-mediated cytolysis in human vaginal (HMVII) and monkey kidney (VERO) epithelial cell lineages. These results highlight the antiparasitic potential of Cu-phendione by interaction with important T. vaginalis virulence factors.
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Affiliation(s)
- Graziela Vargas Rigo
- Faculdade de Farmácia and Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre 90610-000, RS, Brazil
| | - Fernanda Gomes Cardoso
- Faculdade de Farmácia and Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre 90610-000, RS, Brazil
| | - Matheus Mendonça Pereira
- CIEPQPF, Department of Chemical Engineering, University of Coimbra, Rua Sílvio Lima, Pólo II-Pinhal de Marrocos, 3030-790 Coimbra, Portugal
| | - Michael Devereux
- The Inorganic Pharmaceutical and Biomimetic Research Centre, Focas Research Institute, Dublin Institute of Technology, D08 CKP1 Dublin, Ireland
| | - Malachy McCann
- Chemistry Department, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Ireland
| | - André L S Santos
- Laboratório de Estudos Avançados de Microrganismos Emergentes e Resistentes (LEAMER), Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil
| | - Tiana Tasca
- Faculdade de Farmácia and Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre 90610-000, RS, Brazil
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Jacobo-Delgado YM, Rodríguez-Carlos A, Serrano CJ, Rivas-Santiago B. Mycobacterium tuberculosis cell-wall and antimicrobial peptides: a mission impossible? Front Immunol 2023; 14:1194923. [PMID: 37266428 PMCID: PMC10230078 DOI: 10.3389/fimmu.2023.1194923] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 04/25/2023] [Indexed: 06/03/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) is one of the most important infectious agents worldwide and causes more than 1.5 million deaths annually. To make matters worse, the drug resistance among Mtb strains has risen substantially in the last few decades. Nowadays, it is not uncommon to find patients infected with Mtb strains that are virtually resistant to all antibiotics, which has led to the urgent search for new molecules and therapies. Over previous decades, several studies have demonstrated the efficiency of antimicrobial peptides to eliminate even multidrug-resistant bacteria, making them outstanding candidates to counterattack this growing health problem. Nevertheless, the complexity of the Mtb cell wall makes us wonder whether antimicrobial peptides can effectively kill this persistent Mycobacterium. In the present review, we explore the complexity of the Mtb cell wall and analyze the effectiveness of antimicrobial peptides to eliminate the bacilli.
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10
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Sieradzki ET, Nuccio EE, Pett-Ridge J, Firestone MK. Expression of macromolecular organic nitrogen degrading enzymes identifies potential mediators of soil organic N availability to an annual grass. THE ISME JOURNAL 2023:10.1038/s41396-023-01402-3. [PMID: 37059820 DOI: 10.1038/s41396-023-01402-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 03/09/2023] [Accepted: 03/20/2023] [Indexed: 04/16/2023]
Abstract
Nitrogen (N) is frequently limiting to plant growth, in part because most soil N is present as polymeric organic compounds that are not readily taken up by plants. Microbial depolymerization of these large macromolecular N-substrates gradually releases available inorganic N. While many studies have researched and modeled controls on soil organic matter formation and bulk N mineralization, the ecological-spatial, temporal and phylogenetic-patterns underlying organic N degradation remain unclear. We analyzed 48 time-resolved metatranscriptomes and quantified N-depolymerization gene expression to resolve differential expression by soil habitat and time in specific taxonomic groups and gene-based guilds. We observed much higher expression of extracellular serine-type proteases than other extracellular N-degrading enzymes, with protease expression of predatory bacteria declining with time and other taxonomic patterns driven by the presence (Gammaproteobacteria) or absence (Thermoproteota) of live roots and root detritus (Deltaproteobacteria and Fungi). The primary chitinase chit1 gene was more highly expressed by eukaryotes near root detritus, suggesting predation of fungi. In some lineages, increased gene expression over time suggests increased competitiveness with rhizosphere age (Chloroflexi). Phylotypes from some genera had protease expression patterns that could benefit plant N nutrition, for example, we identified a Janthinobacterium phylotype and two Burkholderiales that depolymerize organic N near young roots and a Rhizobacter with elevated protease levels near mature roots. These taxon-resolved gene expression results provide an ecological read-out of microbial interactions and controls on N dynamics in specific soil microhabitats and could be used to target potential plant N bioaugmentation strategies.
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Affiliation(s)
- Ella T Sieradzki
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA.
- Laboratoire Ampère, École Centrale de Lyon, Lyon, France.
| | - Erin E Nuccio
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Life & Environmental Sciences Department, University of California Merced, Merced, CA, USA
| | - Mary K Firestone
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA.
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Saticioglu IB, Ay H, Altun S, Karakaya E, Gunduz ES, Aydogdu D, Yarim D, Erkek N, Duman M. Genomic insight into Myroides oncorhynchi sp. nov., a new member of the Myroides genus, isolated from the internal organ of rainbow trout (Oncorhynchus mykiss). Antonie Van Leeuwenhoek 2023; 116:291-302. [PMID: 36586048 DOI: 10.1007/s10482-022-01804-x] [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: 10/06/2022] [Accepted: 12/24/2022] [Indexed: 01/01/2023]
Abstract
The strain M-43T was isolated from the Oncorhynchus mykiss from a fish farm in Mugla, Turkey. Pairwise 16S rRNA gene sequence analysis was used to identify strain M-43T. The strain was a member of the genus Myroides sharing the highest 16S rRNA gene sequence identity levels of 98.7%, 98.3%, and 98.3% with the type strains of M. profundi D25T, M. odoratimimus subsp. odoratimimus CCUG 39352T and M. odoratimimus subsp. xuanwuensis DSM27251T, respectively. A polyphasic taxonomic approach including whole genome-based analyses was employed to confirm the taxonomic provenance of strain M-43T within the genus Myroides. The overall genome relatedness indices (OGRI) for strain M-43T compared with its most closely related type strains M. odoratimimus subsp. xuanwuensis DSM 27251T, M. profundi D25T, and M. odoratimimus subsp. odoratimimus ATCC BAA-634T, were calculated as 25.3%, 25.1%, and 25% for digital DNA-DNA hybridization (dDDH), 83.3%, 83.6%, and 83.4% for average nucleotide identity (ANI) analyses, respectively. The OGRI values between strain M-43T and its close neighbors confirmed that the strain represents a novel species in the genus Myroides. The DNA G + C content of the strain is 33.7%. The major fatty acids are iso-C15:0 and summed feature 9 (iso-C17:1 ω9c and/or 10-methyl C16:0). The predominant polar lipids are phosphatidylethanolamine, an amino-lipid and five unidentified lipids. The major respiratory quinone is MK-6. Chemotaxonomic and phylogenomic analyses of this isolate confirmed that the strain represents a novel species for which the name Myroides oncorhynchi sp. nov. is proposed, with M-43T as the type strain (JCM 34205T = KCTC 82265T).
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Affiliation(s)
- Izzet Burcin Saticioglu
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Erciyes University, 38280, Kayseri, Turkey.
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Bursa Uludag University, 16059, Bursa, Turkey.
| | - Hilal Ay
- Department of Molecular Biology and Genetics, Faculty of Science, Ondokuz Mayis University, 55139, Samsun, Turkey
| | - Soner Altun
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Bursa Uludag University, 16059, Bursa, Turkey
| | - Emre Karakaya
- Department of Microbiology, Faculty of Veterinary Medicine, Erciyes University, 38280, Kayseri, Turkey
| | - Enes Said Gunduz
- Department of Microbiology, Faculty of Veterinary Medicine, Erciyes University, 38280, Kayseri, Turkey
| | - Duygu Aydogdu
- Department of Microbiology, Faculty of Veterinary Medicine, Erciyes University, 38280, Kayseri, Turkey
| | - Dogancan Yarim
- Department of Microbiology, Faculty of Veterinary Medicine, Erciyes University, 38280, Kayseri, Turkey
| | - Neslihan Erkek
- Department of Microbiology, Faculty of Veterinary Medicine, Erciyes University, 38280, Kayseri, Turkey
| | - Muhammed Duman
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Bursa Uludag University, 16059, Bursa, Turkey
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12
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Saati-Santamaría Z, Baroncelli R, Rivas R, García-Fraile P. Comparative Genomics of the Genus Pseudomonas Reveals Host- and Environment-Specific Evolution. Microbiol Spectr 2022; 10:e0237022. [PMID: 36354324 PMCID: PMC9769992 DOI: 10.1128/spectrum.02370-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 10/24/2022] [Indexed: 11/12/2022] Open
Abstract
Each Earth ecosystem has unique microbial communities. Pseudomonas bacteria have evolved to occupy a plethora of different ecological niches, including living hosts, such as animals and plants. Many genes necessary for the Pseudomonas-niche interaction and their encoded functions remain unknown. Here, we describe a comparative genomic study of 3,274 genomes with 19,056,667 protein-coding sequences from Pseudomonas strains isolated from diverse environments. We detected functional divergence of Pseudomonas that depends on the niche. Each group of strains from a certain environment harbored a distinctive set of metabolic pathways or functions. The horizontal transfer of genes, which mainly proceeded between closely related taxa, was dependent on the isolation source. Finally, we detected thousands of undescribed proteins and functions associated with each Pseudomonas lifestyle. This research represents an effort to reveal the mechanisms underlying the ecology, pathogenicity, and evolution of Pseudomonas, and it will enable clinical, ecological, and biotechnological advances. IMPORTANCE Microbes play important roles in the health of living beings and in the environment. The knowledge of these functions may be useful for the development of new clinical and biotechnological applications and the restoration and preservation of natural ecosystems. However, most mechanisms implicated in the interaction of microbes with the environment remain poorly understood; thus, this field of research is very important. Here, we try to understand the mechanisms that facilitate the differential adaptation of Pseudomonas-a large and ubiquitous bacterial genus-to the environment. We analyzed more than 3,000 Pseudomonas genomes and searched for genetic patterns that can be related with their coevolution with different hosts (animals, plants, or fungi) and environments. Our results revealed that thousands of genes and genetic features are associated with each niche. Our data may be useful to develop new technical and theoretical advances in the fields of ecology, health, and industry.
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Affiliation(s)
- Zaki Saati-Santamaría
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Institute for Agribiotechnology Research (CIALE), Villamayor, Salamanca, Spain
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská, Prague, Czech Republic
| | - Riccardo Baroncelli
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Bologna, Italy
| | - Raúl Rivas
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Institute for Agribiotechnology Research (CIALE), Villamayor, Salamanca, Spain
- Associated Research Unit of Plant-Microorganism Interaction, USAL-CSIC (IRNASA), Salamanca, Spain
| | - Paula García-Fraile
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Institute for Agribiotechnology Research (CIALE), Villamayor, Salamanca, Spain
- Associated Research Unit of Plant-Microorganism Interaction, USAL-CSIC (IRNASA), Salamanca, Spain
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13
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Orata FD, Hussain NAS, Liang KYH, Hu D, Boucher YF. Genomes of Vibrio metoecus co-isolated with Vibrio cholerae extend our understanding of differences between these closely related species. Gut Pathog 2022; 14:42. [PMID: 36404338 PMCID: PMC9677704 DOI: 10.1186/s13099-022-00516-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 11/04/2022] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Vibrio cholerae, the causative agent of cholera, is a well-studied species, whereas Vibrio metoecus is a recently described close relative that is also associated with human infections. The availability of V. metoecus genomes provides further insight into its genetic differences from V. cholerae. Additionally, both species have been co-isolated from a cholera-free brackish coastal pond and have been suggested to interact with each other by horizontal gene transfer (HGT). RESULTS The genomes of 17 strains from each species were sequenced. All strains share a large core genome (2675 gene families) and very few genes are unique to each species (< 3% of the pan-genome of both species). This led to the identification of potential molecular markers-for nitrite reduction, as well as peptidase and rhodanese activities-to further distinguish V. metoecus from V. cholerae. Interspecies HGT events were inferred in 21% of the core genes and 45% of the accessory genes. A directional bias in gene transfer events was found in the core genome, where V. metoecus was a recipient of three times (75%) more genes from V. cholerae than it was a donor (25%). CONCLUSION V. metoecus was misclassified as an atypical variant of V. cholerae due to their resemblance in a majority of biochemical characteristics. More distinguishing phenotypic assays can be developed based on the discovery of potential gene markers to avoid any future misclassifications. Furthermore, differences in relative abundance or seasonality were observed between the species and could contribute to the bias in directionality of HGT.
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Affiliation(s)
- Fabini D. Orata
- grid.17089.370000 0001 2190 316XDepartment of Biological Sciences, University of Alberta, Edmonton, Alberta Canada ,grid.17089.370000 0001 2190 316XDepartment of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta Canada
| | - Nora A. S. Hussain
- grid.17089.370000 0001 2190 316XDepartment of Biological Sciences, University of Alberta, Edmonton, Alberta Canada
| | - Kevin Y. H. Liang
- grid.17089.370000 0001 2190 316XDepartment of Biological Sciences, University of Alberta, Edmonton, Alberta Canada ,grid.14709.3b0000 0004 1936 8649Department of Quantitative Life Sciences, McGill University, Montréal, Québec Canada ,grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada
| | - Dalong Hu
- grid.4280.e0000 0001 2180 6431Saw Swee Hock School of Public Health, National University of Singapore and National University Hospital System, Singapore, Singapore ,grid.4280.e0000 0001 2180 6431Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
| | - Yann F. Boucher
- grid.17089.370000 0001 2190 316XDepartment of Biological Sciences, University of Alberta, Edmonton, Alberta Canada ,grid.4280.e0000 0001 2180 6431Saw Swee Hock School of Public Health, National University of Singapore and National University Hospital System, Singapore, Singapore ,grid.4280.e0000 0001 2180 6431Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore ,grid.4280.e0000 0001 2180 6431Infectious Diseases Translational Research Program, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore and National University Hospital System, Singapore, Singapore
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14
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Zhao D, Chong Y, Hu J, Zhou X, Xiao C, Chen W. Proteomics and metagenomics reveal the relationship between microbial metabolism and protein hydrolysis in dried fermented grass carp using a lactic acid bacteria starter culture. Curr Res Food Sci 2022; 5:2316-2328. [DOI: 10.1016/j.crfs.2022.11.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/21/2022] [Accepted: 11/17/2022] [Indexed: 11/27/2022] Open
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15
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Oda K, Dunn BM, Wlodawer A. Serine-Carboxyl Peptidases, Sedolisins: From Discovery to Evolution. Biochemistry 2022; 61:1643-1664. [PMID: 35862020 DOI: 10.1021/acs.biochem.2c00239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Sedolisin is a proteolytic enzyme, listed in the peptidase database MEROPS as a founding member of clan SB, family S53. This enzyme, although active at low pH, was originally shown not to be inhibited by an aspartic peptidase specific inhibitor, S-PI (pepstatin Ac). In this Perspective, the S53 family is described from the moment of original identification to evolution. The representative enzymes of the family are sedolisin, kumamolisin, and TPP-1. They exhibit the following unique features. (1) The fold of the molecule is similar to that of subtilisin, but the catalytic residues consist of a triad, Ser/Glu/Asp, that is unlike the Ser/His/Asp triad of subtilisin. (2) The molecule is expressed as a pro-form composed of the amino-terminal prosegment and the active domain. Additionally, some members of this family have an additional, carboxy-terminal prosegment. (3) Their optimum pH for activity is in the acidic region, not in the neutral to alkaline region where subtilisin is active. (4) Their distribution in nature is very broad across the three kingdoms of life. (5) Some of these enzymes from fungi and bacteria are pathogens to plants. (6) Some of them have significant potential applications for industry. (7) The lack of a TPP-1 gene in human brain is the cause of incurable juvenile neuronal ceroid lipofuscinosis (Batten's disease).
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Affiliation(s)
- Kohei Oda
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Ben M Dunn
- Department of Biochemistry & Molecular Biology, University of Florida College of Medicine, Gainesville, Florida 32610-0245, United States
| | - Alexander Wlodawer
- Center for Structural Biology, National Cancer Institute, Frederick, Maryland 21702, United States
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16
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A Dual Enrichment Strategy Provides Soil- and Digestate-Competent Nitrous Oxide-Respiring Bacteria for Mitigating Climate Forcing in Agriculture. mBio 2022; 13:e0078822. [PMID: 35638872 PMCID: PMC9239227 DOI: 10.1128/mbio.00788-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Manipulating soil metabolism through heavy inoculation with microbes is feasible if organic wastes can be utilized as the substrate for growth and vector as a fertilizer. This, however, requires organisms active in both digestate and soil (generalists). Here, we present a dual enrichment strategy to enrich and isolate such generalists among N2O-respiring bacteria (NRB) in soil and digestates, to be used as an inoculum for strengthening the N2O-reduction capacity of soils. The enrichment strategy utilizes sequential batch enrichment cultures alternating between sterilized digestate and soil as substrates, with each batch initiated with limited O2 and unlimited N2O. The cultures were monitored for gas kinetics and community composition. As predicted by a Lotka-Volterra competition model, cluster analysis identified generalist operational taxonomic units (OTUs) which became dominant, digestate/soil-specialists which did not, and a majority that were gradually diluted out. We isolated several NRBs circumscribed by generalist OTUs. Their denitrification genes and phenotypes predicted a variable capacity to act as N2O-sinks, while all genomes predicted broad catabolic capacity. The latter contrasts with previous attempts to enrich NRB by anaerobic incubation of unsterilized digestate only, which selected for organisms with a catabolic capacity limited to fermentation products. The two isolates with the most promising characteristics as N2O sinks were aPseudomonas sp. with a full-fledged denitrification-pathway and a Cloacibacterium sp. carrying only N2O reductase (clade II), and soil experiments confirmed their capacity to reduce N2O-emissions from soil. The successful enrichment of NRB with broad catabolic spectra suggests that the concept of dual enrichment should also be applicable for enrichment of generalists with traits other than N2O reduction.
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17
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Cai M, Duan C, Zhang X, Pan J, Liu Y, Zhang C, Li M. Genomic and transcriptomic dissection of Theionarchaea in marine ecosystem. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1222-1234. [PMID: 34668130 DOI: 10.1007/s11427-021-1996-x] [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: 07/20/2021] [Accepted: 08/17/2021] [Indexed: 11/24/2022]
Abstract
Theionarchaea is a recently described archaeal class within the Euryarchaeota. While it is widely distributed in sediment ecosystems, little is known about its metabolic potential and ecological features. Here, we used metagenomics and metatranscriptomics to characterize 12 theionarchaeal metagenome-assembled genomes, which were further divided into two subgroups, from coastal mangrove sediments of China and seawater columns of the Yap Trench. Genomic analysis revealed that apart from the canonical sulfhydrogenase, Theionarchaea harbor genes encoding heliorhodopsin, group 4 [NiFe]-hydrogenase, and flagellin, in which genes for heliorhodopsin and group 4 [NiFe]-hydrogenase were transcribed in mangrove sediment. Further, the theionarchaeal substrate spectrum may be broader than previously reported as revealed by metagenomics and metatranscriptomics, and the potential carbon substrates include detrital proteins, hemicellulose, ethanol, and CO2. The genes for organic substrate metabolism (mainly detrital protein and amino acid metabolism genes) have relatively higher transcripts in the top sediment layers in mangrove wetlands. In addition, co-occurrence analysis suggested that the degradation of these organic compounds by Theionarchaea might be processed in syntrophy with fermenters (e.g., Chloroflexi) and methanogens. Collectively, these observations expand the current knowledge of the metabolic potential of Theionarchaea, and shed light on the metabolic strategies and roles of these archaea in the marine ecosystems.
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Affiliation(s)
- Mingwei Cai
- Archaeal Biology Center, Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Changhai Duan
- Archaeal Biology Center, Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
- SZU-HKUST Joint PhD Program in Marine Environmental Science, Shenzhen University, Shenzhen, 518060, China
| | - Xinxu Zhang
- Archaeal Biology Center, Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Jie Pan
- Archaeal Biology Center, Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Yang Liu
- Archaeal Biology Center, Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Cuijing Zhang
- Archaeal Biology Center, Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Meng Li
- Archaeal Biology Center, Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China.
- SZU-HKUST Joint PhD Program in Marine Environmental Science, Shenzhen University, Shenzhen, 518060, China.
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18
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Genomic Insights into the Distribution of Peptidases and Proteolytic Capacity among Prevotella and Paraprevotella Species. Microbiol Spectr 2022; 10:e0218521. [PMID: 35377228 PMCID: PMC9045265 DOI: 10.1128/spectrum.02185-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Bacterial peptidases play important roles in health and nutrient digestion in both humans and animals, especially ruminant animals. In this study, we examined and compared the various peptidases (both total and secretory) among species of Prevotella (44 in total) and Paraprevotella (2) revealed in their sequenced genomes that were archived in the MEROPS database. The phylogenetic relationships were also compared among the species based on 16S rRNA gene sequences and the occurrence of peptidases. A rich repertoire of peptidases was found that represents six catalytic types of peptidases (aspartic, cysteine, glutamic, metallo, mixed, and serine), together with some with unknown catalytic mechanisms, and 78 families. Metallopeptidases were the most predominant, followed by serine and cysteine peptidases. Considerable variations in peptidase occurrence and distribution were noted among the species and the different families of peptidases. A total of 48 different families of secretory peptidases were found in the genomes of the Prevotella and Paraprevotella species. Secretory peptidases in the families of S41 and M13 were ubiquitous, and S9, M16, C1, S13, and C69 were found in more than 95% of the species. Multivariate analysis of the peptidases indicated that species were mostly clustered except for a few species. Analysis using a bipartite association network showed that the majority of peptidase families were shared among the species. The relatedness of peptidase distributions among the species did not significantly correlate with their phylogenetic relationship based on the 16S rRNA genes. The genomic overview on the peptidases of Prevotella and Paraprevotella species provided new insights into their potential capacity to degrade proteins. IMPORTANCE Species of Prevotella are prevalent and predominant bacteria residing in animals and humans, and their proteolytic capacity and activity play important roles in nutrient utilization in animals (especially ruminants) and some anaerobic infections of the intestinal, respiratory, and urinary tracts in humans. This study reveals the large repertoire and wide distribution of metallo, serine, and cysteine peptidases, especially secretory peptidases, among the Prevotella species. The information presented here could aid in the identification of the Prevotella species and the peptidases to target to decrease the excessive protein degradation in the rumen and improve dietary nitrogen utilization by ruminant animals.
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19
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Maxwell TL, Canarini A, Bogdanovic I, Böckle T, Martin V, Noll L, Prommer J, Séneca J, Simon E, Piepho HP, Herndl M, Pötsch EM, Kaiser C, Richter A, Bahn M, Wanek W. Contrasting drivers of belowground nitrogen cycling in a montane grassland exposed to a multifactorial global change experiment with elevated CO 2 , warming, and drought. GLOBAL CHANGE BIOLOGY 2022; 28:2425-2441. [PMID: 34908205 DOI: 10.5281/zenodo.5597021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 10/26/2021] [Accepted: 11/28/2021] [Indexed: 05/26/2023]
Abstract
Depolymerization of high-molecular weight organic nitrogen (N) represents the major bottleneck of soil N cycling and yet is poorly understood compared to the subsequent inorganic N processes. Given the importance of organic N cycling and the rise of global change, we investigated the responses of soil protein depolymerization and microbial amino acid consumption to increased temperature, elevated atmospheric CO2 , and drought. The study was conducted in a global change facility in a managed montane grassland in Austria, where elevated CO2 (eCO2 ) and elevated temperature (eT) were stimulated for 4 years, and were combined with a drought event. Gross protein depolymerization and microbial amino acid consumption rates (alongside with gross organic N mineralization and nitrification) were measured using 15 N isotope pool dilution techniques. Whereas eCO2 showed no individual effect, eT had distinct effects which were modulated by season, with a negative effect of eT on soil organic N process rates in spring, neutral effects in summer, and positive effects in fall. We attribute this to a combination of changes in substrate availability and seasonal temperature changes. Drought led to a doubling of organic N process rates, which returned to rates found under ambient conditions within 3 months after rewetting. Notably, we observed a shift in the control of soil protein depolymerization, from plant substrate controls under continuous environmental change drivers (eT and eCO2 ) to controls via microbial turnover and soil organic N availability under the pulse disturbance (drought). To the best of our knowledge, this is the first study which analyzed the individual versus combined effects of multiple global change factors and of seasonality on soil organic N processes and thereby strongly contributes to our understanding of terrestrial N cycling in a future world.
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Affiliation(s)
- Tania L Maxwell
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, Center of Microbiology and Environmental Systems Science, Vienna, Austria
- INRAE, Bordeaux Sciences Agro, ISPA, Villenave d'Ornon, France
| | - Alberto Canarini
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, Center of Microbiology and Environmental Systems Science, Vienna, Austria
| | - Ivana Bogdanovic
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, Center of Microbiology and Environmental Systems Science, Vienna, Austria
| | - Theresa Böckle
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, Center of Microbiology and Environmental Systems Science, Vienna, Austria
| | - Victoria Martin
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, Center of Microbiology and Environmental Systems Science, Vienna, Austria
| | - Lisa Noll
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, Center of Microbiology and Environmental Systems Science, Vienna, Austria
| | - Judith Prommer
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, Center of Microbiology and Environmental Systems Science, Vienna, Austria
| | - Joana Séneca
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, Center of Microbiology and Environmental Systems Science, Vienna, Austria
| | - Eva Simon
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, Center of Microbiology and Environmental Systems Science, Vienna, Austria
| | - Hans-Peter Piepho
- Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
| | - Markus Herndl
- Agricultural Research and Education Centre Raumberg-Gumpenstein, Irdning-Donnersbachtal, Austria
| | - Erich M Pötsch
- Agricultural Research and Education Centre Raumberg-Gumpenstein, Irdning-Donnersbachtal, Austria
| | - Christina Kaiser
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, Center of Microbiology and Environmental Systems Science, Vienna, Austria
| | - Andreas Richter
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, Center of Microbiology and Environmental Systems Science, Vienna, Austria
| | - Michael Bahn
- Department of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Wolfgang Wanek
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, Center of Microbiology and Environmental Systems Science, Vienna, Austria
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20
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Maxwell TL, Canarini A, Bogdanovic I, Böckle T, Martin V, Noll L, Prommer J, Séneca J, Simon E, Piepho H, Herndl M, Pötsch EM, Kaiser C, Richter A, Bahn M, Wanek W. Contrasting drivers of belowground nitrogen cycling in a montane grassland exposed to a multifactorial global change experiment with elevated CO 2 , warming, and drought. GLOBAL CHANGE BIOLOGY 2022; 28:2425-2441. [PMID: 34908205 PMCID: PMC9306501 DOI: 10.1111/gcb.16035] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 10/26/2021] [Accepted: 11/28/2021] [Indexed: 05/13/2023]
Abstract
Depolymerization of high-molecular weight organic nitrogen (N) represents the major bottleneck of soil N cycling and yet is poorly understood compared to the subsequent inorganic N processes. Given the importance of organic N cycling and the rise of global change, we investigated the responses of soil protein depolymerization and microbial amino acid consumption to increased temperature, elevated atmospheric CO2 , and drought. The study was conducted in a global change facility in a managed montane grassland in Austria, where elevated CO2 (eCO2 ) and elevated temperature (eT) were stimulated for 4 years, and were combined with a drought event. Gross protein depolymerization and microbial amino acid consumption rates (alongside with gross organic N mineralization and nitrification) were measured using 15 N isotope pool dilution techniques. Whereas eCO2 showed no individual effect, eT had distinct effects which were modulated by season, with a negative effect of eT on soil organic N process rates in spring, neutral effects in summer, and positive effects in fall. We attribute this to a combination of changes in substrate availability and seasonal temperature changes. Drought led to a doubling of organic N process rates, which returned to rates found under ambient conditions within 3 months after rewetting. Notably, we observed a shift in the control of soil protein depolymerization, from plant substrate controls under continuous environmental change drivers (eT and eCO2 ) to controls via microbial turnover and soil organic N availability under the pulse disturbance (drought). To the best of our knowledge, this is the first study which analyzed the individual versus combined effects of multiple global change factors and of seasonality on soil organic N processes and thereby strongly contributes to our understanding of terrestrial N cycling in a future world.
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Affiliation(s)
- Tania L. Maxwell
- Division of Terrestrial Ecosystem ResearchDepartment of Microbiology and Ecosystem ScienceCenter of Microbiology and Environmental Systems ScienceViennaAustria
- INRAEBordeaux Sciences AgroISPAVillenave d'OrnonFrance
| | - Alberto Canarini
- Division of Terrestrial Ecosystem ResearchDepartment of Microbiology and Ecosystem ScienceCenter of Microbiology and Environmental Systems ScienceViennaAustria
| | - Ivana Bogdanovic
- Division of Terrestrial Ecosystem ResearchDepartment of Microbiology and Ecosystem ScienceCenter of Microbiology and Environmental Systems ScienceViennaAustria
| | - Theresa Böckle
- Division of Terrestrial Ecosystem ResearchDepartment of Microbiology and Ecosystem ScienceCenter of Microbiology and Environmental Systems ScienceViennaAustria
| | - Victoria Martin
- Division of Terrestrial Ecosystem ResearchDepartment of Microbiology and Ecosystem ScienceCenter of Microbiology and Environmental Systems ScienceViennaAustria
| | - Lisa Noll
- Division of Terrestrial Ecosystem ResearchDepartment of Microbiology and Ecosystem ScienceCenter of Microbiology and Environmental Systems ScienceViennaAustria
| | - Judith Prommer
- Division of Terrestrial Ecosystem ResearchDepartment of Microbiology and Ecosystem ScienceCenter of Microbiology and Environmental Systems ScienceViennaAustria
| | - Joana Séneca
- Division of Terrestrial Ecosystem ResearchDepartment of Microbiology and Ecosystem ScienceCenter of Microbiology and Environmental Systems ScienceViennaAustria
| | - Eva Simon
- Division of Terrestrial Ecosystem ResearchDepartment of Microbiology and Ecosystem ScienceCenter of Microbiology and Environmental Systems ScienceViennaAustria
| | | | - Markus Herndl
- Agricultural Research and Education Centre Raumberg‐GumpensteinIrdning‐DonnersbachtalAustria
| | - Erich M. Pötsch
- Agricultural Research and Education Centre Raumberg‐GumpensteinIrdning‐DonnersbachtalAustria
| | - Christina Kaiser
- Division of Terrestrial Ecosystem ResearchDepartment of Microbiology and Ecosystem ScienceCenter of Microbiology and Environmental Systems ScienceViennaAustria
| | - Andreas Richter
- Division of Terrestrial Ecosystem ResearchDepartment of Microbiology and Ecosystem ScienceCenter of Microbiology and Environmental Systems ScienceViennaAustria
| | - Michael Bahn
- Department of EcologyUniversity of InnsbruckInnsbruckAustria
| | - Wolfgang Wanek
- Division of Terrestrial Ecosystem ResearchDepartment of Microbiology and Ecosystem ScienceCenter of Microbiology and Environmental Systems ScienceViennaAustria
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21
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Ramírez-Larrota JS, Eckhard U. An Introduction to Bacterial Biofilms and Their Proteases, and Their Roles in Host Infection and Immune Evasion. Biomolecules 2022; 12:306. [PMID: 35204806 PMCID: PMC8869686 DOI: 10.3390/biom12020306] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/03/2022] [Accepted: 02/10/2022] [Indexed: 12/15/2022] Open
Abstract
Bacterial biofilms represent multicellular communities embedded in a matrix of extracellular polymeric substances, conveying increased resistance against environmental stress factors but also antibiotics. They are shaped by secreted enzymes such as proteases, which can aid pathogenicity by degrading host proteins of the connective tissue or the immune system. Importantly, both secreted proteases and the capability of biofilm formation are considered key virulence factors. In this review, we focus on the basic aspects of proteolysis and protein secretion, and highlight various secreted bacterial proteases involved in biofilm establishment and dispersal, and how they aid bacteria in immune evasion by degrading immunoglobulins and components of the complement system. Thus, secreted proteases represent not only prominent antimicrobial targets but also enzymes that can be used for dedicated applications in biotechnology and biomedicine, including their use as laundry detergents, in mass spectrometry for the glycoprofiling of antibodies, and the desensitization of donor organs intended for positive crossmatch patients.
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Affiliation(s)
| | - Ulrich Eckhard
- Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Baldiri Reixac, 15-21, 08028 Barcelona, Spain;
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22
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Jee S, Kang IJ, Bak G, Kang S, Lee J, Heu S, Hwang I. Comparative Genomic Analysis of Pathogenic Factors of Pectobacterium Species Isolated in South Korea Using Whole-Genome Sequencing. THE PLANT PATHOLOGY JOURNAL 2022; 38:12-24. [PMID: 35144358 PMCID: PMC8831359 DOI: 10.5423/ppj.ft.09.2021.0147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/15/2021] [Accepted: 12/21/2021] [Indexed: 06/14/2023]
Abstract
In this study, we conducted whole-genome sequencing with six species of Pectobacterium composed of seven strains, JR1.1, BP201601.1, JK2.1, HNP201719, MYP201603, PZ1, and HC, for the analysis of pathogenic factors associated with the genome of Pectobacterium. The genome sizes ranged from 4,724,337 bp to 5,208,618 bp, with the GC content ranging from 50.4% to 52.3%. The average nucleotide identity was 98% among the two Pectobacterium species and ranged from 88% to 96% among the remaining six species. A similar distribution was observed in the carbohydrate-active enzymes (CAZymes) class and extracellular plant cell wall degrading enzymes (PCWDEs). HC showed the highest number of enzymes in CAZymes and the lowest number in the extracellular PCWDEs. Six strains showed four subsets, and HC demonstrated three subsets, except hasDEF, in type I secretion system, while the type II secretion system of the seven strains was conserved. Components of human pathogens, such as Salmonella pathogenicity island 1 type type III secretion system (T3SS) and effectors, were identified in PZ1; T3SSa was not identified in HC. Two putative effectors, including hrpK, were identified in seven strains along with dspEF. We also identified 13 structural genes, six regulator genes, and five accessory genes in the type VI secretion system (T6SS) gene cluster of six Pectobacterium species, along with the loss of T6SS in PZ1. HC had two subsets, and JK2.1 had three subsets of T6SS. With the GxSxG motif, the phospholipase A gene did locate among tssID and duf4123 genes in the T6SSa cluster of all strains. Important domains were identified in the vgrG/paar islands, including duf4123, duf2235, vrr-nuc, and duf3396.
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Affiliation(s)
- Samnyu Jee
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang 25342,
Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826,
Korea
| | - In-Jeong Kang
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826,
Korea
- Division of Crop Cultivation and Environment Research, National Institute of Crop Science, Suwon 16613,
Korea
| | - Gyeryeong Bak
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang 25342,
Korea
| | - Sera Kang
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang 25342,
Korea
| | - Jeongtae Lee
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang 25342,
Korea
| | - Sunggi Heu
- Department of Plant Science, College of Agriculture and Life Science, Seoul National University, Seoul 08826,
Korea
| | - Ingyu Hwang
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826,
Korea
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23
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Degradation of biological macromolecules supports uncultured microbial populations in Guaymas Basin hydrothermal sediments. THE ISME JOURNAL 2021; 15:3480-3497. [PMID: 34112968 PMCID: PMC8630151 DOI: 10.1038/s41396-021-01026-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 05/26/2021] [Accepted: 05/27/2021] [Indexed: 02/05/2023]
Abstract
Hydrothermal sediments contain large numbers of uncultured heterotrophic microbial lineages. Here, we amended Guaymas Basin sediments with proteins, polysaccharides, nucleic acids or lipids under different redox conditions and cultivated heterotrophic thermophiles with the genomic potential for macromolecule degradation. We reconstructed 20 metagenome-assembled genomes (MAGs) of uncultured lineages affiliating with known archaeal and bacterial phyla, including endospore-forming Bacilli and candidate phylum Marinisomatota. One Marinisomatota MAG had 35 different glycoside hydrolases often in multiple copies, seven extracellular CAZymes, six polysaccharide lyases, and multiple sugar transporters. This population has the potential to degrade a broad spectrum of polysaccharides including chitin, cellulose, pectin, alginate, chondroitin, and carrageenan. We also describe thermophiles affiliating with the genera Thermosyntropha, Thermovirga, and Kosmotoga with the capability to make a living on nucleic acids, lipids, or multiple macromolecule classes, respectively. Several populations seemed to lack extracellular enzyme machinery and thus likely scavenged oligo- or monomers (e.g., MAGs affiliating with Archaeoglobus) or metabolic products like hydrogen (e.g., MAGs affiliating with Thermodesulfobacterium or Desulforudaceae). The growth of methanogens or the production of methane was not observed in any condition, indicating that the tested macromolecules are not degraded into substrates for methanogenesis in hydrothermal sediments. We provide new insights into the niches, and genomes of microorganisms that actively degrade abundant necromass macromolecules under oxic, sulfate-reducing, and fermentative thermophilic conditions. These findings improve our understanding of the carbon flow across trophic levels and indicate how primary produced biomass sustains complex and productive ecosystems.
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24
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Kumari M, Padhi S, Sharma S, Phukon LC, Singh SP, Rai AK. Biotechnological potential of psychrophilic microorganisms as the source of cold-active enzymes in food processing applications. 3 Biotech 2021; 11:479. [PMID: 34790503 DOI: 10.1007/s13205-021-03008-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/29/2021] [Indexed: 12/13/2022] Open
Abstract
Microorganisms striving in extreme environments and exhibiting optimal growth and reproduction at low temperatures, otherwise known as psychrophilic microorganisms, are potential sources of cold-active enzymes. Owing to higher stability and cold activity, these enzymes are gaining enormous attention in numerous industrial bioprocesses. Applications of several cold-active enzymes have been established in the food industry, e.g., β-galactosidase, pectinase, proteases, amylases, xylanases, pullulanases, lipases, and β-mannanases. The enzyme engineering approaches and the accumulating knowledge of protein structure and function have made it possible to improve the catalytic properties of interest and express the candidate enzyme in a heterologous host for a higher level of enzyme production. This review compiles the relevant and recent information on the potential uses of different cold-active enzymes in the food industry.
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Affiliation(s)
- Megha Kumari
- Institute of Bioresources and Sustainable Development, Regional Centre, Sikkim, India
| | - Srichandan Padhi
- Institute of Bioresources and Sustainable Development, Regional Centre, Sikkim, India
| | - Swati Sharma
- Institute of Bioresources and Sustainable Development, Regional Centre, Sikkim, India
| | - Loreni Chiring Phukon
- Institute of Bioresources and Sustainable Development, Regional Centre, Sikkim, India
| | - Sudhir P Singh
- Centre of Innovative and Applied Bioprocessing, Mohali, India
| | - Amit Kumar Rai
- Institute of Bioresources and Sustainable Development, Regional Centre, Sikkim, India
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25
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Abstract
The human skin is our outermost layer and serves as a protective barrier against external insults. Advances in next generation sequencing have enabled the discoveries of a rich and diverse community of microbes - bacteria, fungi and viruses that are residents of this surface. The genomes of these microbes also revealed the presence of many secretory enzymes. In particular, proteases which are hydrolytic enzymes capable of protein cleavage and degradation are of special interest in the skin environment which is enriched in proteins and lipids. In this minireview, we will focus on the roles of these skin-relevant microbial secreted proteases, both in terms of their widely studied roles as pathogenic agents in tissue invasion and host immune inactivation, and their recently discovered roles in inter-microbial interactions and modulation of virulence factors. From these studies, it has become apparent that while microbial proteases are capable of a wide range of functions, their expression is tightly regulated and highly responsive to the environments the microbes are in. With the introduction of new biochemical and bioinformatics tools to study protease functions, it will be important to understand the roles played by skin microbial secretory proteases in cutaneous health, especially the less studied commensal microbes with an emphasis on contextual relevance.
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26
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Kapitány A, Medgyesi B, Jenei A, Somogyi O, Szabó L, Gáspár K, Méhes G, Hendrik Z, Dócs K, Szücs P, Dajnoki Z, Szegedi A. Regional Differences in the Permeability Barrier of the Skin-Implications in Acantholytic Skin Diseases. Int J Mol Sci 2021; 22:ijms221910428. [PMID: 34638769 PMCID: PMC8509001 DOI: 10.3390/ijms221910428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/15/2021] [Accepted: 09/23/2021] [Indexed: 11/01/2022] Open
Abstract
The chemical milieu, microbiota composition, and immune activity show prominent differences in distinct healthy skin areas. The objective of the current study was to compare the major permeability barrier components (stratum corneum and tight junction (TJ)), investigate the distribution of (corneo)desmosomes and TJs, and measure barrier function in healthy sebaceous gland-rich (SGR), apocrine gland-rich (AGR), and gland-poor (GP) skin regions. Molecules involved in cornified envelope (CE) formation, desquamation, and (corneo)desmosome and TJ organization were investigated at the mRNA and protein levels using qRT-PCR and immunohistochemistry. The distribution of junction structures was visualized using confocal microscopy. Transepidermal water loss (TEWL) functional measurements were also performed. CE intracellular structural components were similarly expressed in gland-rich (SGR and AGR) and GP areas. In contrast, significantly lower extracellular protein levels of (corneo)desmosomes (DSG1 and CDSN) and TJs (OCLN and CLDN1) were detected in SGR/AGR areas compared to GP areas. In parallel, kallikrein proteases were significantly higher in gland-rich regions. Moreover, gland-rich areas were characterized by prominently disorganized junction structures ((corneo)desmosomes and TJs) and significantly higher TEWL levels compared to GP skin, which exhibited a regular distribution of junction structures. According to our findings, the permeability barrier of our skin is not uniform. Gland-rich areas are characterized by weaker permeability barrier features compared with GP regions. These findings have important clinical relevance and may explain the preferred localization of acantholytic skin diseases on gland-rich skin regions (e.g., Pemphigus foliaceus, Darier's disease, and Hailey-Hailey disease).
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Affiliation(s)
- Anikó Kapitány
- Division of Dermatological Allergology, Department of Dermatology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (A.K.); (B.M.); (A.J.); (O.S.); (L.S.); (K.G.); (Z.D.)
- Department of Dermatology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Barbara Medgyesi
- Division of Dermatological Allergology, Department of Dermatology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (A.K.); (B.M.); (A.J.); (O.S.); (L.S.); (K.G.); (Z.D.)
- Department of Dermatology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
- Gyula Petrányi Doctoral School of Allergy and Clinical Immunology, University of Debrecen, 4032 Debrecen, Hungary
| | - Adrienn Jenei
- Division of Dermatological Allergology, Department of Dermatology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (A.K.); (B.M.); (A.J.); (O.S.); (L.S.); (K.G.); (Z.D.)
- Department of Dermatology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
- Gyula Petrányi Doctoral School of Allergy and Clinical Immunology, University of Debrecen, 4032 Debrecen, Hungary
| | - Orsolya Somogyi
- Division of Dermatological Allergology, Department of Dermatology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (A.K.); (B.M.); (A.J.); (O.S.); (L.S.); (K.G.); (Z.D.)
- Department of Dermatology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
- Gyula Petrányi Doctoral School of Allergy and Clinical Immunology, University of Debrecen, 4032 Debrecen, Hungary
| | - Lilla Szabó
- Division of Dermatological Allergology, Department of Dermatology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (A.K.); (B.M.); (A.J.); (O.S.); (L.S.); (K.G.); (Z.D.)
- Department of Dermatology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
- Gyula Petrányi Doctoral School of Allergy and Clinical Immunology, University of Debrecen, 4032 Debrecen, Hungary
| | - Krisztián Gáspár
- Division of Dermatological Allergology, Department of Dermatology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (A.K.); (B.M.); (A.J.); (O.S.); (L.S.); (K.G.); (Z.D.)
- Department of Dermatology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Gábor Méhes
- Department of Pathology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary;
| | - Zoltán Hendrik
- Department of Forensic Medicine, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary;
| | - Klaudia Dócs
- Department of Anatomy, Histology and Embryology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (K.D.); (P.S.)
| | - Péter Szücs
- Department of Anatomy, Histology and Embryology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (K.D.); (P.S.)
| | - Zsolt Dajnoki
- Division of Dermatological Allergology, Department of Dermatology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (A.K.); (B.M.); (A.J.); (O.S.); (L.S.); (K.G.); (Z.D.)
- Department of Dermatology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Andrea Szegedi
- Division of Dermatological Allergology, Department of Dermatology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (A.K.); (B.M.); (A.J.); (O.S.); (L.S.); (K.G.); (Z.D.)
- Department of Dermatology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
- Correspondence: ; Tel.: +36-52-411-717/56432
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Tancos MA, McMahon MB, Garrett WM, Luster DG, Rogers EE. Comparative Secretome Analyses of Toxigenic and Atoxigenic Rathayibacter Species. PHYTOPATHOLOGY 2021; 111:1530-1540. [PMID: 33499664 DOI: 10.1094/phyto-11-20-0495-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Phytopathogenic Rathayibacter species are unique bacterial plant pathogens because they are obligately vectored by plant parasitic anguinid nematodes to the developing seedheads of forage grasses and cereals. This understudied group of plant-associated Actinomycetes includes the neurotoxigenic plant pathogen R. toxicus, which causes annual ryegrass toxicity in grazing livestock. R. toxicus is currently endemic to Australia and is listed as a plant pathogen select agent by the U.S. Department of Agriculture-Animal and Plant Health Inspection Service. The complex Rathayibacter disease cycle requires intimate interactions with the nematode vector and plant hosts, which warrants an increased understanding of the secretory and surface-associated proteins that mediate these diverse eukaryotic interactions. Here we present the first comparative secretome analysis for this complex, nematode-vectored Rathayibacter genus that compares the three agronomically damaging toxigenic and atoxigenic Rathayibacter species, R. toxicus, R. iranicus, and R. tritici. The exoproteomic comparison identified 1,423 unique proteins between the three species via liquid chromatography-tandem mass spectrometry, leading to the identification of putative pathogenicity-related proteins and proteins that may mediate nematode attachment. Of the uniquely identified proteins, 94 homologous proteins were conserved between the three Rathayibacter exoproteomes and comprised between 43.4 and 58.6% of total protein abundance. Comparative analyses revealed both conserved and uniquely expressed extracellular proteins, which, interestingly, had more similarities to extracellular proteins commonly associated with bacterial animal pathogens than classic plant pathogens. This comparative exoproteome analysis will facilitate the characterization of proteins essential for vector attachment and host colonization and assist in the development of serological diagnostic assays.
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Affiliation(s)
- Matthew A Tancos
- Foreign Disease-Weed Science Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Frederick, MD
| | - Michael B McMahon
- Foreign Disease-Weed Science Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Frederick, MD
| | - Wesley M Garrett
- Animal Biosciences and Biotechnology Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD
| | - Douglas G Luster
- Foreign Disease-Weed Science Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Frederick, MD
| | - Elizabeth E Rogers
- Foreign Disease-Weed Science Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Frederick, MD
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28
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Zhang D, Zhu Z, Li Y, Li X, Guan Z, Zheng J. Comparative Genomics of Exiguobacterium Reveals What Makes a Cosmopolitan Bacterium. mSystems 2021; 6:e0038321. [PMID: 34282940 PMCID: PMC8407118 DOI: 10.1128/msystems.00383-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/28/2021] [Indexed: 11/20/2022] Open
Abstract
Although the strategies used by bacteria to adapt to specific environmental conditions are widely reported, fewer studies have addressed how microbes with a cosmopolitan distribution can survive in diverse ecosystems. Exiguobacterium is a versatile genus whose members are commonly found in various habitats. To better understand the mechanisms underlying the universality of Exiguobacterium, we collected 105 strains from diverse environments and performed large-scale metabolic and adaptive ability tests. We found that most Exiguobacterium members have the capacity to survive under wide ranges of temperature, salinity, and pH. According to phylogenetic and average nucleotide identity analyses, we identified 27 putative species and classified two genetic groups: groups I and II. Comparative genomic analysis revealed that the Exiguobacterium members utilize a variety of complex polysaccharides and proteins to support survival in diverse environments and also employ a number of chaperonins and transporters for this purpose. We observed that the group I species can be found in more diverse terrestrial environments and have a larger genome size than the group II species. Our analyses revealed that the expansion of transporter families drove genomic expansion in group I strains, and we identified 25 transporter families, many of which are involved in the transport of important substrates and resistance to environmental stresses and are enriched in group I strains. This study provides important insights into both the overall general genetic basis for the cosmopolitan distribution of a bacterial genus and the evolutionary and adaptive strategies of Exiguobacterium. IMPORTANCE The wide distribution characteristics of Exiguobacterium make it a valuable model for studying the adaptive strategies of bacteria that can survive in multiple habitats. In this study, we reveal that members of the Exiguobacterium genus have a cosmopolitan distribution and share an extensive adaptability that enables them to survive in various environments. The capacities shared by Exiguobacterium members, such as their diverse means of polysaccharide utilization and environmental-stress resistance, provide an important basis for their cosmopolitan distribution. Furthermore, the selective expansion of transporter families has been a main driving force for genomic evolution in Exiguobacterium. Our findings improve our understanding of the adaptive and evolutionary mechanisms of cosmopolitan bacteria and the vital genomic traits that can facilitate niche adaptation.
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Affiliation(s)
- Dechao Zhang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Zhaolu Zhu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Yangjie Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Xudong Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Ziyu Guan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Jinshui Zheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
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29
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An Integrative Bioinformatic Analysis for Keratinase Detection in Marine-Derived Streptomyces. Mar Drugs 2021; 19:md19060286. [PMID: 34063876 PMCID: PMC8224001 DOI: 10.3390/md19060286] [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: 04/14/2021] [Revised: 05/12/2021] [Accepted: 05/18/2021] [Indexed: 01/08/2023] Open
Abstract
Keratinases present promising biotechnological applications, due to their ability to degrade keratin. Streptomyces appears as one of the main sources of these enzymes, but complete genome sequences of keratinolytic bacteria are still limited. This article reports the complete genomes of three marine-derived streptomycetes that show different levels of feather keratin degradation, with high (strain G11C), low (strain CHD11), and no (strain Vc74B-19) keratinolytic activity. A multi-step bioinformatics approach is described to explore genes encoding putative keratinases in these genomes. Despite their differential keratinolytic activity, multiplatform annotation reveals similar quantities of ORFs encoding putative proteases in strains G11C, CHD11, and Vc74B-19. Comparative genomics classified these putative proteases into 140 orthologous groups and 17 unassigned orthogroup peptidases belonging to strain G11C. Similarity network analysis revealed three network communities of putative peptidases related to known keratinases of the peptidase families S01, S08, and M04. When combined with the prediction of cellular localization and phylogenetic reconstruction, seven putative keratinases from the highly keratinolytic strain Streptomyces sp. G11C are identified. To our knowledge, this is the first multi-step bioinformatics analysis that complements comparative genomics with phylogeny and cellular localization prediction, for the prediction of genes encoding putative keratinases in streptomycetes.
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30
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Li QM, Zhou YL, Wei ZF, Wang Y. Phylogenomic Insights into Distribution and Adaptation of Bdellovibrionota in Marine Waters. Microorganisms 2021; 9:757. [PMID: 33916768 PMCID: PMC8067016 DOI: 10.3390/microorganisms9040757] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/26/2021] [Accepted: 04/01/2021] [Indexed: 11/23/2022] Open
Abstract
Bdellovibrionota is composed of obligate predators that can consume some Gram-negative bacteria inhabiting various environments. However, whether genomic traits influence their distribution and marine adaptation remains to be answered. In this study, we performed phylogenomics and comparative genomics studies using 132 Bdellovibrionota genomes along with five metagenome-assembled genomes (MAGs) from deep sea zones. Four phylogenetic groups, Oligoflexia, Bdello-group1, Bdello-group2 and Bacteriovoracia, were revealed by constructing a phylogenetic tree, of which 53.84% of Bdello-group2 and 48.94% of Bacteriovoracia were derived from the ocean. Bacteriovoracia was more prevalent in deep sea zones, whereas Bdello-group2 was largely distributed in the epipelagic zone. Metabolic reconstruction indicated that genes involved in chemotaxis, flagellar (mobility), type II secretion system, ATP-binding cassette (ABC) transporters and penicillin-binding protein were necessary for the predatory lifestyle of Bdellovibrionota. Genes involved in glycerol metabolism, hydrogen peroxide (H2O2) degradation, cell wall recycling and peptide utilization were ubiquitously present in Bdellovibrionota genomes. Comparative genomics between marine and non-marine Bdellovibrionota demonstrated that betaine as an osmoprotectant is probably widely used by marine Bdellovibrionota, and all the marine genomes have a number of genes for adaptation to marine environments. The genes encoding chitinase and chitin-binding protein were identified for the first time in Oligoflexia, which implied that Oligoflexia may prey on a wider spectrum of microbes. This study expands our knowledge on adaption strategies of Bdellovibrionota inhabiting deep seas and the potential usage of Oligoflexia for biological control.
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Affiliation(s)
- Qing-Mei Li
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; (Q.-M.L.); (Y.-L.Z.); (Z.-F.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying-Li Zhou
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; (Q.-M.L.); (Y.-L.Z.); (Z.-F.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhan-Fei Wei
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; (Q.-M.L.); (Y.-L.Z.); (Z.-F.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong Wang
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; (Q.-M.L.); (Y.-L.Z.); (Z.-F.W.)
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Kõiv V, Tenson T. Gluten-degrading bacteria: availability and applications. Appl Microbiol Biotechnol 2021; 105:3045-3059. [PMID: 33837830 PMCID: PMC8053163 DOI: 10.1007/s00253-021-11263-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/18/2021] [Accepted: 03/31/2021] [Indexed: 12/11/2022]
Abstract
Gluten is a mixture of storage proteins in wheat and occurs in smaller amounts in other cereal grains. It provides favorable structure to bakery products but unfortunately causes disease conditions with increasing prevalence. In the human gastrointestinal tract, gluten is cleaved into proline and gluten rich peptides that are not degraded further. These peptides trigger immune responses that might lead to celiac disease, wheat allergy, and non-celiac gluten sensitivity. The main treatment option is a gluten-free diet. Alternatively, using enzymes or microorganisms with gluten-degrading properties might alleviate the disease. These components can be used during food production or could be introduced into the digestive tract as food supplements. In addition, natural food from the environment is known to enrich the microbial communities in gut and natural environmental microbial communities have high potential to degrade gluten. It remains to be investigated if food and environment-induced changes in the gut microbiome could contribute to the triggering of gluten-related diseases. KEY POINTS: • Wheat proteins, gluten, are incompletely digested in human digestive tract leading to gluten intolerance. • The only efficient treatment of gluten intolerance is life-long gluten-free diet. • Environmental bacteria acquired together with food could be source of gluten-degrading bacteria detoxifying undigested gluten peptides.
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Affiliation(s)
- Viia Kõiv
- Institute of Technology, University of Tartu, Tartu, Estonia.
| | - Tanel Tenson
- Institute of Technology, University of Tartu, Tartu, Estonia
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Tahon G, Lebbe L, Willems A. Spirosoma utsteinense sp. nov. isolated from Antarctic ice-free soils from the Utsteinen region, East Antarctica. Int J Syst Evol Microbiol 2021; 71. [PMID: 33729126 DOI: 10.1099/ijsem.0.004754] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Between 2014 and 2016, 16 Gram-stain-negative, aerobic, rod-shaped and yellow-orange pigmented bacteria were isolated from exposed soils from the Utsteinen region, Sør Rondane Mountains, East Antarctica. Analysis of their 16S rRNA gene sequences revealed that the strains form a separate cluster in the genus Spirosoma, with Spirosoma rigui KCTC 12531T as its closest neighbour (97.8 % sequence similarity). Comparative genome analysis of two representative strains (i.e. R-68523T and R-68079) of the new group with the type strains of Spirosoma rigui (its closest neighbour) and Spirosoma linguale (type species of the genus), yielded average nucleotide identity values of 73.9-78.7 %. Digital DNA-DNA reassociation values of the two strains and these type strains ranged from 20.3 to 22.0 %. The predominant cellular fatty acids of the two novel strains were summed feature 3 (i.e. C16 : 1 ω7c and/or iso-C15 2-OH), C16 : 1 ω5c, C16 : 0 and iso-C15 : 0. The new Spirosoma strains grew with 0-0.5 % (w/v) NaCl, at pH 6.5-8.0 and displayed optimum growth between 15 and 25 °C. Based on the results of phenotypic, genomic, phylogenetic and chemotaxonomic analyses, the new strains represent a novel species of the genus Spirosoma for which the name Spirosoma utsteinense sp. nov. is proposed. The type strain is R-68523T (=LMG 31447T=CECT 9925T).
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Affiliation(s)
- Guillaume Tahon
- Present address: Laboratory of Microbiology, Agrotechnology and Food Sciences, Wageningen University, Wageningen, Netherlands.,Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Liesbeth Lebbe
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Anne Willems
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
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Mei R, Nobu MK, Narihiro T, Liu WT. Metagenomic and Metatranscriptomic Analyses Revealed Uncultured Bacteroidales Populations as the Dominant Proteolytic Amino Acid Degraders in Anaerobic Digesters. Front Microbiol 2020; 11:593006. [PMID: 33193263 PMCID: PMC7661554 DOI: 10.3389/fmicb.2020.593006] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 10/13/2020] [Indexed: 01/22/2023] Open
Abstract
Current understanding of amino acid (AA) degraders in anaerobic digesters is mainly based on cultured species, whereas microorganisms that play important roles in a complex microbial community remain poorly characterized. This study investigated short-term enrichments degrading single AAs using metagenomics and metatranscriptomics. Metagenomic analysis revealed that populations related to cultured AA degraders had an abundance <2.5% of the sequences. In contrast, metagenomic-assembled bins related to uncultured Bacteroidales collectively accounted for >35% of the sequences. Phylogenetic analyses suggested that these Bacteroidales populations represented a yet-to-be characterized family lineage, i.e., Bacteroidetes vadinHA17. The bins possessed the genetic capacity related to protein degradation, including surface adhesion (3–7 genes), secreted peptidase (52–77 genes), and polypeptide-specific transporters (2–5 genes). Furthermore, metatranscriptomics revealed that these Bacteroidales populations expressed the complete metabolic pathways for degrading 16 to 17 types of AAs in enrichments fed with respective substrates. These characteristics were distinct from cultured AA degraders including Acidaminobacter and Peptoclostridium, suggesting the uncultured Bacteroidales were the major protein-hydrolyzing and AA-degrading populations. These uncultured Bacteroidales were further found to be dominant and active in full-scale anaerobic digesters, indicating their important ecological roles in the native habitats. “Candidatus Aminobacteroidaceae” was proposed to represent the previously uncharted family Bacteroidetes vadinHA17.
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Affiliation(s)
- Ran Mei
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Masaru K Nobu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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Kmeck A, Tancer RJ, Ventura CR, Wiedman GR. Synergies with and Resistance to Membrane-Active Peptides. Antibiotics (Basel) 2020; 9:antibiotics9090620. [PMID: 32961656 PMCID: PMC7559582 DOI: 10.3390/antibiotics9090620] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/07/2020] [Accepted: 09/17/2020] [Indexed: 12/12/2022] Open
Abstract
Membrane-active peptides (MAPs) have long been thought of as the key to defeating antimicrobial-resistant microorganisms. Such peptides, however, may not be sufficient alone. In this review, we seek to highlight some of the common pathways for resistance, as well as some avenues for potential synergy. This discussion takes place considering resistance, and/or synergy in the extracellular space, at the membrane, and during interaction, and/or removal. Overall, this review shows that researchers require improved definitions of resistance and a more thorough understanding of MAP-resistance mechanisms. The solution to combating resistance may ultimately come from an understanding of how to harness the power of synergistic drug combinations.
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Microbiome of root vegetables-a source of gluten-degrading bacteria. Appl Microbiol Biotechnol 2020; 104:8871-8885. [PMID: 32875365 PMCID: PMC7502452 DOI: 10.1007/s00253-020-10852-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/29/2020] [Accepted: 08/23/2020] [Indexed: 12/11/2022]
Abstract
Abstract Gluten is a cereal protein that is incompletely digested by human proteolytic enzymes that create immunogenic peptides that accumulate in the gastrointestinal tract (GIT). Although both environmental and human bacteria have been shown to expedite gluten hydrolysis, gluten intolerance is a growing concern. Here we hypothesize that together with food, we acquire environmental bacteria that could impact our GIT with gluten-degrading bacteria. Using in vitro gastrointestinal simulation conditions, we evaluated the capacity of endophytic bacteria that inhabit root vegetables, potato (Solanum tuberosum), carrot (Daucus sativus), beet (Beta vulgaris), and topinambur (Jerusalem artichoke) (Helianthus tuberosus), to resist these conditions and degrade gluten. By 16S rDNA sequencing, we discovered that bacteria from the families Enterobacteriaceae, Bacillaceae, and Clostridiaceae most effectively multiply in conditions similar to the human GIT (microoxic conditions, 37 °C) while utilizing vegetable material and gluten as nutrients. Additionally, we used stomach simulation (1 h, pH 3) and intestinal simulation (1 h, bile salts 0.4%) treatments. The bacteria that survived this treatment retained the ability to degrade gluten epitopes but at lower levels. Four bacterial strains belonging to species Bacillus pumilus, Clostridium subterminale, and Clostridium sporogenes isolated from vegetable roots produced proteases with postproline cleaving activity that successfully neutralized the toxic immunogenic epitopes. Key points • Bacteria from root vegetables can degrade gluten. • Some of these bacteria can resist conditions mimicking gastrointestinal tract. Electronic supplementary material The online version of this article (10.1007/s00253-020-10852-0) contains supplementary material, which is available to authorized users.
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Shvarev D, Maldener I. The HlyD-like membrane fusion protein All5304 is essential for acid stress survival of the filamentous cyanobacterium Anabaena sp. PCC 7120. FEMS Microbiol Lett 2020; 367:5863934. [PMID: 32592389 DOI: 10.1093/femsle/fnaa108] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 06/25/2020] [Indexed: 12/23/2022] Open
Abstract
Acid stress is an environmental problem for plants and fresh water cyanobacteria like the filamentous, heterocyst forming species Anabaena sp. PCC 7120 (hereafter Anabaena sp.). Heterocyst differentiation, cell-cell communication and nitrogen fixation has been deeply studied in this model organism, but little is known about the cellular response of Anabaena sp. to decreased pH values, causing acid stress. ATP-binding cassette (ABC) transporters are involved in acid stress response in other bacteria, by exporting proteins responsible for survival under acidification. The genome of Anabaena sp. encodes numerous ABC transporter components, whose function is not known yet. Here, we describe the function of the gene all5304 encoding a protein with homology to membrane fusion proteins of tripartite efflux pumps driven by ABC transporters like HlyBD-TolC of Escherichia coli. The all5304 mutant shows less resistance against low pH, even though the expression of the gene is independent from the pH of the medium. We compared the exoproteome of the wild type and mutant cultures and identified three proteins-candidate substrates of the putative transporter. Including the in silico analysis of All5304, our results suggest that All5304 functions as part of an efflux pump, secreting of a protein necessary for acid tolerance in Anabaena sp.
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Affiliation(s)
- Dmitry Shvarev
- Organismic Interactions, Interfaculty Institute of Microbiology and Infection Medicine, Eberhard Karls University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Iris Maldener
- Organismic Interactions, Interfaculty Institute of Microbiology and Infection Medicine, Eberhard Karls University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
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Perfumo A, Freiherr von Sass GJ, Nordmann EL, Budisa N, Wagner D. Discovery and Characterization of a New Cold-Active Protease From an Extremophilic Bacterium via Comparative Genome Analysis and in vitro Expression. Front Microbiol 2020; 11:881. [PMID: 32528424 PMCID: PMC7247812 DOI: 10.3389/fmicb.2020.00881] [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: 12/08/2019] [Accepted: 04/16/2020] [Indexed: 01/05/2023] Open
Abstract
Following a screening of Antarctic glacier forefield-bacteria for novel cold-active enzymes, a psychrophilic strain Psychrobacter sp. 94-6PB was selected for further characterization of enzymatic activities. The strain produced lipases and proteases in the temperature range of 4-18°C. The coding sequence of an extracellular serine-protease was then identified via comparative analysis across Psychrobacter sp. genomes, PCR-amplified in our strain 94-6PB and expressed in the heterologous host E. coli. The purified enzyme (80 kDa) resulted to be a cold-active alkaline protease, performing best at temperatures of 20-30°C and pH 7-9. It was stable in presence of common inhibitors [β-mercaptoethanol (β-ME), dithiothreitol (DTT), urea, phenylmethylsulfonyl fluoride (PMSF) and ethylenediaminetetraacetic acid (EDTA)] and compatible with detergents and surfactants (Tween 20, Tween 80, hydrogen peroxide and Triton X-100). Because of these properties, the P94-6PB protease may be suitable for use in a new generation of laundry products for cold washing. Furthermore, we assessed the microdiversity of this enzyme in Psychrobacter organisms from different cold habitats and found several gene clusters that correlated with specific ecological niches. We then discussed the role of habitat specialization in shaping the biodiversity of proteins and enzymes and anticipate far-reaching implications for the search of novel variants of biotechnological products.
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Affiliation(s)
- Amedea Perfumo
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section Geomicrobiology, Potsdam, Germany
- Polar Terrestrial Environmental System Division, Helmholtz Centre for Polar and Marine Research, Alfred Wegener Institute, Potsdam, Germany
| | | | - Eva-Lena Nordmann
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section Geomicrobiology, Potsdam, Germany
- Institute of Chemistry and Biology of the Marine Environment, Carl-von-Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Nediljko Budisa
- Institute of Chemistry, Technische Universität Berlin, Berlin, Germany
- Institute of Chemistry, University of Manitoba, Winnipeg, MB, Canada
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section Geomicrobiology, Potsdam, Germany
- Institute of Geosciences, University of Potsdam, Potsdam, Germany
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Aliyu H, Gorte O, Zhou X, Neumann A, Ochsenreither K. In silico Proteomic Analysis Provides Insights Into Phylogenomics and Plant Biomass Deconstruction Potentials of the Tremelalles. Front Bioeng Biotechnol 2020; 8:226. [PMID: 32318549 PMCID: PMC7147457 DOI: 10.3389/fbioe.2020.00226] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 03/05/2020] [Indexed: 01/27/2023] Open
Abstract
Basidiomycetes populate a wide range of ecological niches but unlike ascomycetes, their capabilities to decay plant polymers and their potential for biotechnological approaches receive less attention. Particularly, identification and isolation of CAZymes is of biotechnological relevance and has the potential to improve the cache of currently available commercial enzyme cocktails toward enhanced plant biomass utilization. The order Tremellales comprises phylogenetically diverse fungi living as human pathogens, mycoparasites, saprophytes or associated with insects. Here, we have employed comparative genomics approaches to highlight the phylogenomic relationships among thirty-five Tremellales and to identify putative enzymes of biotechnological interest encoded on their genomes. Evaluation of the predicted proteomes of the thirty-five Tremellales revealed 6,918 putative carbohydrate-active enzymes (CAZYmes) and 7,066 peptidases. Two soil isolates, Saitozyma podzolica DSM 27192 and Cryptococcus sp. JCM 24511, show higher numbers harboring an average of 317 compared to a range of 267-121 CAZYmes for the rest of the strains. Similarly, the proteomes of the two soil isolates along with two plant associated strains contain higher number of peptidases sharing an average of 234 peptidases compared to a range of 226-167 for the rest of the strains. Despite these huge differences and the apparent enrichment of these enzymes among the soil isolates, the data revealed a diversity of the various enzyme families that does not reflect specific habitat type. Growth experiment on various carbohydrates to validate the predictions provides support for this view. Overall, the data indicates that the Tremellales could serve as a rich source of both CAZYmes and peptidases with wide range of potential biotechnological relevance.
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Affiliation(s)
- Habibu Aliyu
- Institute of Process Engineering in Life Science 2: Technical Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Olga Gorte
- Institute of Process Engineering in Life Science 2: Technical Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Xinhai Zhou
- Institute of Process Engineering in Life Science 2: Technical Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Anke Neumann
- Institute of Process Engineering in Life Science 2: Technical Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Katrin Ochsenreither
- Institute of Process Engineering in Life Science 2: Technical Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
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Lavrentyeva EV, Erdyneeva EB, Dunaevskii YE, Boltyanskaya YV, Kevbrin VV. Peptidase Activity of Proteinivorax Bacteria and Their Possible Ecological Role in the Microbial Communities of Tanatar Soda Lakes (Altai Krai, Russia). Microbiology (Reading) 2020. [DOI: 10.1134/s0026261719060079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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