1
|
Chadwick GL, Dury GA, Nayak DD. Physiological and transcriptomic response to methyl-coenzyme M reductase limitation in Methanosarcina acetivorans. Appl Environ Microbiol 2024; 90:e0222023. [PMID: 38916294 PMCID: PMC11267899 DOI: 10.1128/aem.02220-23] [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: 12/10/2023] [Accepted: 06/03/2024] [Indexed: 06/26/2024] Open
Abstract
Methyl-coenzyme M reductase (MCR) catalyzes the final step of methanogenesis, the microbial metabolism responsible for nearly all biological methane emissions to the atmosphere. Decades of biochemical and structural research studies have generated detailed insights into MCR function in vitro, yet very little is known about the interplay between MCR and methanogen physiology. For instance, while it is routinely stated that MCR catalyzes the rate-limiting step of methanogenesis, this has not been categorically tested. In this study, to gain a more direct understanding of MCR's control on the growth of Methanosarcina acetivorans, we generate a strain with an inducible mcr operon on the chromosome, allowing for careful control of MCR expression. We show that MCR is not growth rate-limiting in substrate-replete batch cultures. However, through careful titration of MCR expression, growth-limiting state(s) can be obtained. Transcriptomic analysis of M. acetivorans experiencing MCR limitation reveals a global response with hundreds of differentially expressed genes across diverse functional categories. Notably, MCR limitation leads to strong induction of methylsulfide methyltransferases, likely due to insufficient recycling of metabolic intermediates. In addition, the mcr operon is not transcriptionally regulated, i.e., it is constitutively expressed, suggesting that the overabundance of MCR might be beneficial when cells experience nutrient limitation or stressful conditions. Altogether, we show that there is a wide range of cellular MCR concentrations that can sustain optimal growth, suggesting that other factors such as anabolic reactions might be rate-limiting for methanogenic growth. IMPORTANCE Methane is a potent greenhouse gas that has contributed to ca. 25% of global warming in the post-industrial era. Atmospheric methane is primarily of biogenic origin, mostly produced by microorganisms called methanogens. Methyl-coenzyme M reductase (MCR) catalyzes methane formatio in methanogens. Even though MCR comprises ca. 10% of the cellular proteome, it is hypothesized to be growth-limiting during methanogenesis. In this study, we show that Methanosarcina acetivorans cells grown in substrate-replicate batch cultures produce more MCR than its cellular demand for optimal growth. The tools outlined in this study can be used to refine metabolic models of methanogenesis and assay lesions in MCR in a higher-throughput manner than isolation and biochemical characterization of pure protein.
Collapse
Affiliation(s)
- Grayson L. Chadwick
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Gavin A. Dury
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Dipti D. Nayak
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| |
Collapse
|
2
|
Cuervo L, Méndez C, Olano C, Malmierca MG. Volatilome: Smells like microbial spirit. ADVANCES IN APPLIED MICROBIOLOGY 2024; 127:1-43. [PMID: 38763526 DOI: 10.1016/bs.aambs.2024.02.008] [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: 05/21/2024]
Abstract
In recent years, the study of volatile compounds has sparked interest due to their implications in signaling and the enormous variety of bioactive properties attributed to them. Despite the absence of analysis methods standardization, there are a multitude of tools and databases that allow the identification and quantification of volatile compounds. These compounds are chemically heterogeneous and their diverse properties are exploited by various fields such as cosmetics, the food industry, agriculture and medicine, some of which will be discussed here. In virtue of volatile compounds being ubiquitous and fast chemical messengers, these molecules mediate a large number of interspecific and intraspecific interactions, which are key at an ecological level to maintaining the balance and correct functioning of ecosystems. This review briefly summarized the role of volatile compounds in inter- and intra-specific relationships as well as industrial applications associated with the use of these compounds that is emerging as a promising field of study.
Collapse
Affiliation(s)
- Lorena Cuervo
- Functional Biology Department, University of Oviedo, Oviedo, Spain; University Institute of Oncology of Asturias, University of Oviedo, Oviedo, Spain; Health Research Institute of Asturias, Av. del Hospital Universitario, s/n, Oviedo, Spain
| | - Carmen Méndez
- Functional Biology Department, University of Oviedo, Oviedo, Spain; University Institute of Oncology of Asturias, University of Oviedo, Oviedo, Spain; Health Research Institute of Asturias, Av. del Hospital Universitario, s/n, Oviedo, Spain
| | - Carlos Olano
- Functional Biology Department, University of Oviedo, Oviedo, Spain; University Institute of Oncology of Asturias, University of Oviedo, Oviedo, Spain; Health Research Institute of Asturias, Av. del Hospital Universitario, s/n, Oviedo, Spain
| | - Mónica G Malmierca
- Functional Biology Department, University of Oviedo, Oviedo, Spain; University Institute of Oncology of Asturias, University of Oviedo, Oviedo, Spain; Health Research Institute of Asturias, Av. del Hospital Universitario, s/n, Oviedo, Spain.
| |
Collapse
|
3
|
Wilawan B, Chan SS, Ling TC, Show PL, Ng EP, Jonglertjunya W, Phadungbut P, Khoo KS. Advancement of Carotenogenesis of Astaxanthin from Haematococcus pluvialis: Recent Insight and Way Forward. Mol Biotechnol 2024; 66:402-423. [PMID: 37270443 DOI: 10.1007/s12033-023-00768-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 05/07/2023] [Indexed: 06/05/2023]
Abstract
The demand for astaxanthin has been increasing for many health applications ranging from pharmaceuticals, food, cosmetics, and aquaculture due to its bioactive properties. Haematococcus pluvialis is widely recognized as the microalgae species with the highest natural accumulation of astaxanthin, which has made it a valuable source for industrial production. Astaxanthin produced by other sources such as chemical synthesis or fermentation are often produced in the cis configuration, which has been shown to have lower bioactivity. Additionally, some sources of astaxanthin, such as shrimp, may denature or degrade when exposed to high temperatures, which can result in a loss of bioactivity. Producing natural astaxanthin through the cultivation of H. pluvialis is presently a demanding and time-consuming task, which incurs high expenses and restricts the cost-effective industrial production of this valuable substance. The production of astaxanthin occurs through two distinct pathways, namely the cytosolic mevalonate pathway and the chloroplast methylerythritol phosphate (MEP) pathway. The latest advancements in enhancing product quality and extracting techniques at a reasonable cost are emphasized in this review. The comparative of specific extraction processes of H. pluvialis biological astaxanthin production that may be applied to large-scale industries were assessed. The article covers a contemporary approach to optimizing microalgae culture for increased astaxanthin content, as well as obtaining preliminary data on the sustainability of astaxanthin production and astaxanthin marketing information.
Collapse
Affiliation(s)
- Busakorn Wilawan
- Institut Biologi Sains, Fakulti Sains, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
- Department of Chemical Engineering, Faculty of Engineering, Mahidol University, Salaya, Nakhon Pathom, 73170, Thailand
| | - Sook Sin Chan
- Institut Biologi Sains, Fakulti Sains, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Tau Chuan Ling
- Institut Biologi Sains, Fakulti Sains, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Pau Loke Show
- Department of Chemical Engineering, Khalifa University, P.O. Box 127788, Abu Dhabi, United Arab Emirates
- Zhejiang Provincial Key Laboratory for Subtropical Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou, 325035, China
- Department of Chemical and Environmental Engineering, Faculty of Science and Engineering, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor Darul Ehsan, Malaysia
| | - Eng-Poh Ng
- School of Chemical Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - Woranart Jonglertjunya
- Fermentation Technology Laboratory (FerTechLab), Department of Chemical Engineering, Faculty of Engineering, Mahidol University, Nakhon Pathom, 73170, Thailand.
| | - Poomiwat Phadungbut
- Nanocomposite Engineering Laboratory (NanoCEN), Department of Chemical Engineering, Faculty of Engineering, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Kuan Shiong Khoo
- Department of Chemical Engineering and Materials Science, Yuan Ze University, Taoyuan, Taiwan.
- Department of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai, 602105, India.
| |
Collapse
|
4
|
Ma JY, Yan Z, Sun XD, Jiang YQ, Duan JL, Feng LJ, Zhu FP, Liu XY, Xia PF, Yuan XZ. A hybrid photocatalytic system enables direct glucose utilization for methanogenesis. Proc Natl Acad Sci U S A 2024; 121:e2317058121. [PMID: 38232281 PMCID: PMC10823229 DOI: 10.1073/pnas.2317058121] [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: 10/04/2023] [Accepted: 11/20/2023] [Indexed: 01/19/2024] Open
Abstract
Integration of methanogenic archaea with photocatalysts presents a sustainable solution for solar-driven methanogenesis. However, maximizing CH4 conversion efficiency remains challenging due to the intrinsic energy conservation and strictly restricted substrates of methanogenic archaea. Here, we report a solar-driven biotic-abiotic hybrid (biohybrid) system by incorporating cadmium sulfide (CdS) nanoparticles with a rationally designed methanogenic archaeon Methanosarcina acetivorans C2A, in which the glucose synergist protein and glucose kinase, an energy-efficient route for glucose transport and phosphorylation from Zymomonas mobilis, were implemented to facilitate nonnative substrate glucose for methanogenesis. We demonstrate that the photo-excited electrons facilitate membrane-bound electron transport chain, thereby augmenting the Na+ and H+ ion gradients across membrane to enhance adenosine triphosphate (ATP) synthesis. Additionally, this biohybrid system promotes the metabolism of pyruvate to acetyl coenzyme A (AcCoA) and inhibits the flow of AcCoA to the tricarboxylic acid (TCA) cycle, resulting in a 1.26-fold augmentation in CH4 production from glucose-derived carbon. Our results provide a unique strategy for enhancing methanogenesis through rational biohybrid design and reprogramming, which gives a promising avenue for sustainably manufacturing value-added chemicals.
Collapse
Affiliation(s)
- Jing-Ya Ma
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao266237, People’s Republic of China
| | - Zhen Yan
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao266237, People’s Republic of China
| | - Xiao-Dong Sun
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao266237, People’s Republic of China
| | - Yu-Qian Jiang
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao266237, People’s Republic of China
| | - Jian-Lu Duan
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao266237, People’s Republic of China
| | - Li-Juan Feng
- College of Geography and Environment, Shandong Normal University, Jinan250014, People’s Republic of China
| | - Fan-Ping Zhu
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao266237, People’s Republic of China
| | - Xiao-Yu Liu
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao266237, People’s Republic of China
| | - Peng-Fei Xia
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao266237, People’s Republic of China
| | - Xian-Zheng Yuan
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao266237, People’s Republic of China
- Sino-French Research Institute for Ecology and Environment, Shandong University, Qingdao266237, People’s Republic of China
| |
Collapse
|
5
|
Zhu P, Somvanshi T, Bao J, Scheller S. CRISPR/Cas12a toolbox for genome editing in Methanosarcina acetivorans. Front Microbiol 2023; 14:1235616. [PMID: 38149272 PMCID: PMC10750270 DOI: 10.3389/fmicb.2023.1235616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 11/21/2023] [Indexed: 12/28/2023] Open
Abstract
Methanogenic archaea play an important role in the global carbon cycle and may serve as host organisms for the biotechnological production of fuels and chemicals from CO2 and other one-carbon substrates. Methanosarcina acetivorans is extensively studied as a model methanogen due to its large genome, versatile substrate range, and available genetic tools. Genome editing in M. acetivorans via CRISPR/Cas9 has also been demonstrated. Here, we describe a user-friendly CRISPR/Cas12a toolbox that recognizes T-rich (5'-TTTV) PAM sequences. The toolbox can manage deletions of 3,500 bp (i.e., knocking out the entire frhADGB operon) and heterologous gene insertions with positive rates of over 80%. Cas12a-mediated multiplex genome editing was used to edit two separate sites on the chromosome in one round of editing. Double deletions of 100 bp were achieved, with 8/8 of transformants being edited correctly. Simultaneous deletion of 100 bp at one site and replacement of 100 bp with the 2,400 bp uidA expression cassette at a separate site yielded 5/6 correctly edited transformants. Our CRISPR/Cas12a toolbox enables reliable genome editing, and it can be used in parallel with the previously reported Cas9-based system for the genetic engineering of the Methanosarcina species.
Collapse
Affiliation(s)
| | | | - Jichen Bao
- Laboratory of Biochemistry, Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Espoo, Finland
| | - Silvan Scheller
- Laboratory of Biochemistry, Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Espoo, Finland
| |
Collapse
|
6
|
Kulakowski S, Banerjee D, Scown CD, Mukhopadhyay A. Improving microbial bioproduction under low-oxygen conditions. Curr Opin Biotechnol 2023; 84:103016. [PMID: 37924688 DOI: 10.1016/j.copbio.2023.103016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/17/2023] [Accepted: 10/07/2023] [Indexed: 11/06/2023]
Abstract
Microbial bioconversion provides access to a wide range of sustainably produced chemicals and commodities. However, industrial-scale bioproduction process operations are preferred to be anaerobic due to the cost associated with oxygen transfer. Anaerobic bioconversion generally offers limited substrate utilization profiles, lower product yields, and reduced final product diversity compared with aerobic processes. Bioproduction under conditions of reduced oxygen can overcome the limitations of fully aerobic and anaerobic bioprocesses, but many microbial hosts are not developed for low-oxygen bioproduction. Here, we describe advances in microbial strain engineering involving the use of redox cofactor engineering, genome-scale metabolic modeling, and functional genomics to enable improved bioproduction processes under low oxygen and provide a viable path for scaling these bioproduction systems to industrial scales.
Collapse
Affiliation(s)
- Shawn Kulakowski
- Joint BioEnergy Institute, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Deepanwita Banerjee
- Joint BioEnergy Institute, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Corinne D Scown
- Joint BioEnergy Institute, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Energy Analysis and Environmental Impacts Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| |
Collapse
|
7
|
Abstract
Methanogenic archaea are the only organisms that produce CH4 as part of their energy-generating metabolism. They are ubiquitous in oxidant-depleted, anoxic environments such as aquatic sediments, anaerobic digesters, inundated agricultural fields, the rumen of cattle, and the hindgut of termites, where they catalyze the terminal reactions in the degradation of organic matter. Methanogenesis is the only metabolism that is restricted to members of the domain Archaea. Here, we discuss the importance of model organisms in the history of methanogen research, including their role in the discovery of the archaea and in the biochemical and genetic characterization of methanogenesis. We also discuss outstanding questions in the field and newly emerging model systems that will expand our understanding of this uniquely archaeal metabolism.
Collapse
Affiliation(s)
- Kyle C. Costa
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | | |
Collapse
|
8
|
Wang CC, Xie MJ, Zhang R, Cao J, Tang MZ, Xu YX. Improved strength, creep resistance and recyclability of polyisoprene vitrimers by bottom-up construction of inhomogeneous network. POLYMER 2023. [DOI: 10.1016/j.polymer.2023.125854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
|
9
|
Santiago-Martínez MG, Ferry JG. Methods for Culturing Anaerobic Microorganisms. Methods Mol Biol 2023; 2648:231-238. [PMID: 37039994 DOI: 10.1007/978-1-0716-3080-8_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
Anaerobic microorganisms (anaerobes) proliferate in diverse oxygen-free environments. They inhabit Earth's soils and aquatic sediments, the rumen and gut of mammals, and the gut of insects among many other oxygen-free environments. Anaerobes impact biotechnological, biomedical, ecological, and astrobiological fields. Sensitivity to oxygen is of prime consideration for successful culturing which is essential to understand function. Although cultivated for many years, the protocols and media components have been modified and adapted to the special needs of species, as well as conditions and variables for experimental evaluations. Here we describe a revised method used in our laboratories for the growth of methane-producing anaerobes (methanogenic archaea) which are among the most oxygen sensitive. The method is an example for the preparation of more specific media to cultivate a wide diversity of anaerobes.
Collapse
Affiliation(s)
- Michel Geovanni Santiago-Martínez
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA.
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA.
| | - James Gregory Ferry
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| |
Collapse
|
10
|
Carr S, Buan NR. Insights into the biotechnology potential of Methanosarcina. Front Microbiol 2022; 13:1034674. [PMID: 36590411 PMCID: PMC9797515 DOI: 10.3389/fmicb.2022.1034674] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 10/28/2022] [Indexed: 12/23/2022] Open
Abstract
Methanogens are anaerobic archaea which conserve energy by producing methane. Found in nearly every anaerobic environment on earth, methanogens serve important roles in ecology as key organisms of the global carbon cycle, and in industry as a source of renewable biofuels. Environmentally, methanogenic archaea play an essential role in the reintroducing unavailable carbon to the carbon cycle by anaerobically converting low-energy, terminal metabolic degradation products such as one and two-carbon molecules into methane which then returns to the aerobic portion of the carbon cycle. In industry, methanogens are commonly used as an inexpensive source of renewable biofuels as well as serving as a vital component in the treatment of wastewater though this is only the tip of the iceberg with respect to their metabolic potential. In this review we will discuss how the efficient central metabolism of methanoarchaea could be harnessed for future biotechnology applications.
Collapse
Affiliation(s)
| | - Nicole R. Buan
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
| |
Collapse
|
11
|
Lyu Z, Rotaru AE, Pimentel M, Zhang CJ, Rittmann SKMR. Editorial: The methane moment - Cross-boundary significance of methanogens: Preface. Front Microbiol 2022; 13:1055494. [PMID: 36504803 PMCID: PMC9731359 DOI: 10.3389/fmicb.2022.1055494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 10/19/2022] [Indexed: 11/16/2022] Open
Affiliation(s)
- Zhe Lyu
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States,Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, United States,*Correspondence: Zhe Lyu
| | - Amelia-Elena Rotaru
- Nordic Center for Earth Evolution (NORDCEE), University of Southern Denmark, Odense, Denmark,Amelia-Elena Rotaru
| | - Mark Pimentel
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai, Los Angeles, CA, United States,Mark Pimentel
| | - Cui-Jing Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China,Cui-Jing Zhang
| | - Simon K.-M. R. Rittmann
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, Vienna, Austria,Arkeon GmbH, Tulln a.d. Donau, Austria,Simon K.-M. R. Rittmann
| |
Collapse
|
12
|
Total optimization potential (TOP) approach based constrained design of isoprene and cis-abienol production in A. thaliana. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
|
13
|
Bao J, de Dios Mateos E, Scheller S. Efficient CRISPR/Cas12a-Based Genome-Editing Toolbox for Metabolic Engineering in Methanococcus maripaludis. ACS Synth Biol 2022; 11:2496-2503. [PMID: 35730587 PMCID: PMC9295151 DOI: 10.1021/acssynbio.2c00137] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
![]()
The rapid-growing
and genetically tractable methanogen Methanococcus
maripaludis is a promising host organism
for the biotechnological conversion of carbon dioxide and renewable
hydrogen to fuels and value-added products. Expansion of its product
scope through metabolic engineering necessitates reliable and efficient
genetic tools, particularly for genome edits that affect the primary
metabolism and cell growth. Here, we have designed a genome-editing
toolbox by utilizing Cas12a from Lachnospiraceae bacterium ND2006 (LbCas12a) in combination with the homology-directed repair
machinery endogenously present in M. maripaludis. This toolbox can delete target genes with a success rate of up
to 95%, despite the hyperpolyploidy of M. maripaludis. For the purpose of demonstrating a large deletion, the M. maripaludis flagellum operon (∼8.9 kbp)
was replaced by the Escherichia coli β-glucuronidase gene. To facilitate metabolic engineering
and flux balancing in M. maripaludis, the relative strength of 15 different promoters was quantified
in the presence of two common growth substrates, either formate or
carbon dioxide and hydrogen. This CRISPR/LbCas12a toolbox can be regarded
as a reliable and quick method for genome editing in a methanogen.
Collapse
Affiliation(s)
- Jichen Bao
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, FI-02150 Espoo, Finland
| | - Enrique de Dios Mateos
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, FI-02150 Espoo, Finland
| | - Silvan Scheller
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, FI-02150 Espoo, Finland
| |
Collapse
|
14
|
Isar J, Jain D, Joshi H, Dhoot S, Rangaswamy V. MICROBIAL isoprene production: an overview. World J Microbiol Biotechnol 2022; 38:122. [PMID: 35637362 DOI: 10.1007/s11274-022-03306-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 05/09/2022] [Indexed: 11/28/2022]
Abstract
Isoprene, a volatile C5 hydrocarbon, is a precursor of synthetic rubber and an important building block for a variety of natural products, solely being produced by petrochemical routes. To mitigate the ever-increasing contribution of petrochemical industry to global warming through significant carbon (CO2) evolution, bio-based process for isoprene production using microbial cell factories have been explored. Highly efficient fermentation-based processes have been studied for little over a decade now with extensive research on the rational strain development for creating robust strains for commercial isoprene production. Most of these studies involved sugars as feedstocks and using naturally occurring isoprene pathways viz., mevalonate and methyl erythritol pathway in E. coli. Recent advances, driven by efforts in reducing environmental pollution, have focused on utilization of inorganic CO2 by cyanobacteria or syngas from waste gases by acetogens for isoprene production. This review endeavors to capture the latest relevant progress made in rational strain development, metabolic engineering and synthetic biology strategies used, challenges in fermentation process development at lab and commercial scale production of isoprene along with a future perspective pertaining to this area of research.
Collapse
Affiliation(s)
- Jasmine Isar
- High Value Chemicals, Reliance Industries Limited, Reliance Corporate Park, Ghansoli, Navi Mumbai, 400701, India
| | - Dharmendra Jain
- High Value Chemicals, Reliance Industries Limited, Reliance Corporate Park, Ghansoli, Navi Mumbai, 400701, India
| | - Harshvardhan Joshi
- High Value Chemicals, Reliance Industries Limited, Reliance Corporate Park, Ghansoli, Navi Mumbai, 400701, India
| | - Shrikant Dhoot
- High Value Chemicals, Reliance Industries Limited, Reliance Corporate Park, Ghansoli, Navi Mumbai, 400701, India
| | - Vidhya Rangaswamy
- High Value Chemicals, Reliance Industries Limited, Reliance Corporate Park, Ghansoli, Navi Mumbai, 400701, India.
| |
Collapse
|
15
|
Gagliano MC, Sampara P, Plugge CM, Temmink H, Sudmalis D, Ziels RM. Functional Insights of Salinity Stress-Related Pathways in Metagenome-Resolved Methanothrix Genomes. Appl Environ Microbiol 2022; 88:e0244921. [PMID: 35477253 PMCID: PMC9128505 DOI: 10.1128/aem.02449-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 04/11/2022] [Indexed: 12/15/2022] Open
Abstract
Recently, methanogenic archaea belonging to the genus Methanothrix were reported to have a fundamental role in maintaining stable ecosystem functioning in anaerobic bioreactors under different configurations/conditions. In this study, we reconstructed three Methanothrix metagenome-assembled genomes (MAGs) from granular sludge collected from saline upflow anaerobic sludge blanket (UASB) reactors, where Methanothrix harundinacea was previously implicated with the formation of compact and stable granules under elevated salinity levels (up to 20 g/L Na+). Genome annotation and pathway analysis of the Methanothrix MAGs revealed a genetic repertoire supporting their growth under high salinity. Specifically, the most dominant Methanothrix (MAG_279), classified as a subspecies of Methanothrix_A harundinacea_D, had the potential to augment its salinity resistance through the production of different glycoconjugates via the N-glycosylation process, and via the production of compatible solutes as Nε-acetyl-β-lysine and ectoine. The stabilization and reinforcement of the cell membrane via the production of isoprenoids was identified as an additional stress-related pathway in this microorganism. The improved understanding of the salinity stress-related mechanisms of M. harundinacea highlights its ecological niche in extreme conditions, opening new perspectives for high-efficiency methanisation of organic waste at high salinities, as well as the possible persistence of this methanogen in highly-saline natural anaerobic environments. IMPORTANCE Using genome-centric metagenomics, we discovered a new Methanothrix harundinacea subspecies that appears to be a halotolerant acetoclastic methanogen with the flexibility for adaptation in the anaerobic digestion process both at low (5 g/L Na+) and high salinity conditions (20 g/L Na+). Annotation of the recovered M. harundinacea genome revealed salinity stress-related functions, including the modification of EPS glycoconjugates and the production of compatible solutes. This is the first study reporting these genomic features within a Methanothrix sp., a milestone further supporting previous studies that identified M. harundinacea as a key-driver in anaerobic granulation under high salinity stress.
Collapse
Affiliation(s)
- Maria Cristina Gagliano
- Wetsus – European Centre of Excellence for Sustainable Water Technology, Leeuwarden, the Netherlands
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, the Netherlands
| | - Pranav Sampara
- Civil Engineering, University of British Columbia, Vancouver, British Columbia, Canada
| | - Caroline M. Plugge
- Wetsus – European Centre of Excellence for Sustainable Water Technology, Leeuwarden, the Netherlands
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, the Netherlands
| | - Hardy Temmink
- Wetsus – European Centre of Excellence for Sustainable Water Technology, Leeuwarden, the Netherlands
- Department of Environmental Technology, Wageningen University and Research, Wageningen, the Netherlands
| | - Dainis Sudmalis
- Department of Environmental Technology, Wageningen University and Research, Wageningen, the Netherlands
| | - Ryan M. Ziels
- Civil Engineering, University of British Columbia, Vancouver, British Columbia, Canada
| |
Collapse
|
16
|
Danchin A. In vivo, in vitro and in silico: an open space for the development of microbe-based applications of synthetic biology. Microb Biotechnol 2022; 15:42-64. [PMID: 34570957 PMCID: PMC8719824 DOI: 10.1111/1751-7915.13937] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 09/14/2021] [Indexed: 12/24/2022] Open
Abstract
Living systems are studied using three complementary approaches: living cells, cell-free systems and computer-mediated modelling. Progresses in understanding, allowing researchers to create novel chassis and industrial processes rest on a cycle that combines in vivo, in vitro and in silico studies. This design-build-test-learn iteration loop cycle between experiments and analyses combines together physiology, genetics, biochemistry and bioinformatics in a way that keeps going forward. Because computer-aided approaches are not directly constrained by the material nature of the entities of interest, we illustrate here how this virtuous cycle allows researchers to explore chemistry which is foreign to that present in extant life, from whole chassis to novel metabolic cycles. Particular emphasis is placed on the importance of evolution.
Collapse
Affiliation(s)
- Antoine Danchin
- Kodikos LabsInstitut Cochin24 rue du Faubourg Saint‐JacquesParis75014France
| |
Collapse
|
17
|
Innard N, Chong JPJ. The challenges of monitoring and manipulating anaerobic microbial communities. BIORESOURCE TECHNOLOGY 2022; 344:126326. [PMID: 34780902 DOI: 10.1016/j.biortech.2021.126326] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 11/03/2021] [Accepted: 11/09/2021] [Indexed: 06/13/2023]
Abstract
Mixed anaerobic microbial communities are a key component in valorization of waste biomass via anaerobic digestion. Similar microbial communities are important as soil and animal microbiomes and have played a critical role in shaping the planet as it is today. Understanding how individual species within communities interact with others and their environment is important for improving performance and potential applications of an inherently green technology. Here, the challenges associated with making measurements critical to assessing the status of anaerobic microbial communities are considered. How these measurements could be incorporated into control philosophies and augment the potential of anaerobic microbial communities to produce different and higher value products from waste materials are discussed. The benefits and pitfalls of current genetic and molecular approaches to measuring and manipulating anaerobic microbial communities and the challenges which should be addressed to realise the potential of this exciting technology are explored.
Collapse
Affiliation(s)
- Nathan Innard
- Department of Biology, University of York, Wentworth Way, Heslington, York YO10 5DD, UK
| | - James P J Chong
- Department of Biology, University of York, Wentworth Way, Heslington, York YO10 5DD, UK.
| |
Collapse
|
18
|
Contreras G, Thomsen J, Pfitzer M, Hafenbradl D, Kostner D, Holtmann D, Schmitz R, Rother M, Molitor B. New perspectives for biotechnological applications of methanogens. CURRENT RESEARCH IN BIOTECHNOLOGY 2022. [DOI: 10.1016/j.crbiot.2022.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
|
19
|
Carruthers DN, Lee TS. Diversifying Isoprenoid Platforms via Atypical Carbon Substrates and Non-model Microorganisms. Front Microbiol 2021; 12:791089. [PMID: 34925299 PMCID: PMC8677530 DOI: 10.3389/fmicb.2021.791089] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 11/10/2021] [Indexed: 01/07/2023] Open
Abstract
Isoprenoid compounds are biologically ubiquitous, and their characteristic modularity has afforded products ranging from pharmaceuticals to biofuels. Isoprenoid production has been largely successful in Escherichia coli and Saccharomyces cerevisiae with metabolic engineering of the mevalonate (MVA) and methylerythritol phosphate (MEP) pathways coupled with the expression of heterologous terpene synthases. Yet conventional microbial chassis pose several major obstacles to successful commercialization including the affordability of sugar substrates at scale, precursor flux limitations, and intermediate feedback-inhibition. Now, recent studies have challenged typical isoprenoid paradigms by expanding the boundaries of terpene biosynthesis and using non-model organisms including those capable of metabolizing atypical C1 substrates. Conversely, investigations of non-model organisms have historically informed optimization in conventional microbes by tuning heterologous gene expression. Here, we review advances in isoprenoid biosynthesis with specific focus on the synergy between model and non-model organisms that may elevate the commercial viability of isoprenoid platforms by addressing the dichotomy between high titer production and inexpensive substrates.
Collapse
Affiliation(s)
- David N Carruthers
- Joint BioEnergy Institute, Emeryville, CA, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Taek Soon Lee
- Joint BioEnergy Institute, Emeryville, CA, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| |
Collapse
|