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Netrusov AI, Liyaskina EV, Kurgaeva IV, Liyaskina AU, Yang G, Revin VV. Exopolysaccharides Producing Bacteria: A Review. Microorganisms 2023; 11:1541. [PMID: 37375041 DOI: 10.3390/microorganisms11061541] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/31/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Bacterial exopolysaccharides (EPS) are essential natural biopolymers used in different areas including biomedicine, food, cosmetic, petroleum, and pharmaceuticals and also in environmental remediation. The interest in them is primarily due to their unique structure and properties such as biocompatibility, biodegradability, higher purity, hydrophilic nature, anti-inflammatory, antioxidant, anti-cancer, antibacterial, and immune-modulating and prebiotic activities. The present review summarizes the current research progress on bacterial EPSs including their properties, biological functions, and promising applications in the various fields of science, industry, medicine, and technology, as well as characteristics and the isolation sources of EPSs-producing bacterial strains. This review provides an overview of the latest advances in the study of such important industrial exopolysaccharides as xanthan, bacterial cellulose, and levan. Finally, current study limitations and future directions are discussed.
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Affiliation(s)
- Alexander I Netrusov
- Department of Microbiology, Faculty of Biology, M.V. Lomonosov Moscow State University, 119234 Moscow, Russia
- Faculty of Biology and Biotechnology, High School of Economics, 119991 Moscow, Russia
| | - Elena V Liyaskina
- Department of Biotechnology, Biochemistry and Bioengineering, National Research Ogarev Mordovia State University, 430005 Saransk, Russia
| | - Irina V Kurgaeva
- Department of Biotechnology, Biochemistry and Bioengineering, National Research Ogarev Mordovia State University, 430005 Saransk, Russia
| | - Alexandra U Liyaskina
- Institute of the World Ocean, Far Eastern Federal University, 690922 Vladivostok, Russia
| | - Guang Yang
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Viktor V Revin
- Department of Biotechnology, Biochemistry and Bioengineering, National Research Ogarev Mordovia State University, 430005 Saransk, Russia
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2
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Revin VV, Liyas’kina EV, Pokidko BV, Pimenov NV, Mardanov AV, Ravin NV. Characteristics of the New Xanthan-Producing Strain Xanthomonas campestris М 28: Study of the Genome, Cultivation Conditions, and Physicochemical and Rheological Properties of the Polysaccharide. APPL BIOCHEM MICRO+ 2021. [DOI: 10.1134/s0003683821030108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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3
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Acetan and Acetan-Like Polysaccharides: Genetics, Biosynthesis, Structure, and Viscoelasticity. Polymers (Basel) 2021; 13:polym13050815. [PMID: 33799945 PMCID: PMC7961339 DOI: 10.3390/polym13050815] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/01/2021] [Accepted: 03/02/2021] [Indexed: 02/07/2023] Open
Abstract
Bacteria produce a variety of multifunctional polysaccharides, including structural, intracellular, and extracellular polysaccharides. They are attractive for the industrial sector due to their natural origin, sustainability, biodegradability, low toxicity, stability, unique viscoelastic properties, stable cost, and supply. When incorporated into different matrices, they may control emulsification, stabilization, crystallization, water release, and encapsulation. Acetan is an important extracellular water-soluble polysaccharide produced mainly by bacterial species of the genera Komagataeibacter and Acetobacter. Since its original description in Komagataeibacter xylinus, acetan-like polysaccharides have also been described in other species of acetic acid bacteria. Our knowledge on chemical composition of different acetan-like polysaccharides, their viscoelasticity, and the genetic basis for their production has expanded during the last years. Here, we review data on acetan biosynthesis, its molecular structure, genetic organization, and mechanical properties. In addition, we have performed an extended bioinformatic analysis on acetan-like polysaccharide genetic clusters in the genomes of Komagataeibacter and Acetobacter species. The analysis revealed for the first time a second acetan-like polysaccharide genetic cluster, that is widespread in both genera. All species of the Komagataeibacter possess at least one acetan genetic cluster, while it is present in only one third of the Acetobacter species surveyed.
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4
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Sun X, Zhang J. Bacterial exopolysaccharides: Chemical structures, gene clusters and genetic engineering. Int J Biol Macromol 2021; 173:481-490. [PMID: 33493567 DOI: 10.1016/j.ijbiomac.2021.01.139] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 11/25/2022]
Abstract
In recent decades, the composition, structure, biosynthesis, and function of bacterial extracellular polysaccharides (EPS) have been extensively studied. EPS are synthesized through different biosynthetic pathways. The genes responsible for EPS synthesis are usually clustered on the genome or large plasmids of bacteria. Generally, different EPS synthesis gene clusters direct the synthesis of EPS with different chemical structures and biological activities. A better understanding of the gene functions involved in EPS biosynthesis is critical for the production of EPS with special biological activities. Genetic engineering methods are usually used to study EPS synthesis related genes. This review organizes the available information on EPS, including their structures, synthesis of related genes, and highlights the research progress of modifying EPS gene clusters through gene-editing methods.
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Affiliation(s)
- Xiaqing Sun
- Center for Molecular Metabolism, Nanjing University of Science & Technology, Nanjing, China
| | - Jianfa Zhang
- Center for Molecular Metabolism, Nanjing University of Science & Technology, Nanjing, China.
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5
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Távora FTPK, Santos C, Maximiano MR, Murad AM, Oliveira-Neto OB, Megias E, Reis Junior FB, Franco OL, Mehta A. Pan Proteome of Xanthomonas campestris pv. campestris Isolates Contrasting in Virulence. Proteomics 2019; 19:e1900082. [PMID: 31050381 DOI: 10.1002/pmic.201900082] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 03/30/2019] [Indexed: 11/07/2022]
Abstract
Fully sequenced genomes of Xanthomonas campestris pv. campestris (Xcc) strains are reported. However, intra-pathovar differences are still intriguing and far from clear. In this work, the contrasting virulence between two isolates of Xcc - Xcc51 (more virulent) and XccY21 (less virulent) is evaluated by determining their pan proteome profiles. The bacteria are grown in NYG and XVM1 (optimal for induction of hrp regulon) broths and collected at the max-exponential growth phase. Shotgun proteomics reveals a total of 329 proteins when Xcc isolates are grown in XVM1. A comparison of both profiles reveals 47 proteins with significant abundance fluctuations, out of which, 39 show an increased abundance in Xcc51 and are mainly involved in virulence/adaptation mechanisms, genetic information processing, and membrane receptor/iron transport systems, such as BfeA, BtuB, Cap, Clp, Dcp, FyuA, GroEs, HpaG, Tig, and OmpP6. Several differential proteins are further analyzed by qRT-PCR, which reveals a similar expression pattern to the protein abundance. The data shed light on the complex Xcc pathogenicity mechanisms and point out a set of proteins related to the higher virulence of Xcc51. This information is essential for the development of more efficient strategies aiming at the control of black rot disease.
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Affiliation(s)
- Fabiano T P K Távora
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, CEP 70770-917, DF, Brazil.,Departamento de Genética e Biotecnologia, Instituto de Biologia, Universidade Federal de Juiz de Fora, Juiz de Fora, CEP 36036-900, MG, Brazil
| | - Cristiane Santos
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, CEP 70770-917, DF, Brazil.,Departamento de Genética e Biotecnologia, Instituto de Biologia, Universidade Federal de Juiz de Fora, Juiz de Fora, CEP 36036-900, MG, Brazil
| | - Mariana R Maximiano
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, CEP 70770-917, DF, Brazil.,Departamento de Genética e Biotecnologia, Instituto de Biologia, Universidade Federal de Juiz de Fora, Juiz de Fora, CEP 36036-900, MG, Brazil
| | - André M Murad
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, CEP 70770-917, DF, Brazil
| | - Osmundo Brilhante Oliveira-Neto
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, CEP 70770-917, DF, Brazil.,Departamento de Bioquímica e Biologia Molecular, Escola de Medicina, FACIPLAC, Brasília, CEP 72460-000, DF, Brazil
| | - Esaú Megias
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, CEP 70770-917, DF, Brazil
| | | | - Octávio L Franco
- Departamento de Genética e Biotecnologia, Instituto de Biologia, Universidade Federal de Juiz de Fora, Juiz de Fora, CEP 36036-900, MG, Brazil.,Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, CEP 70790-160, DF, Brazil.,S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, CEP 79117-900, MS, Brazil
| | - Angela Mehta
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, CEP 70770-917, DF, Brazil
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6
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Characterisation of barley-associated bacteria and their impact on wort separation performance. JOURNAL OF THE INSTITUTE OF BREWING 2018. [DOI: 10.1002/jib.509] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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7
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Schatschneider S, Schneider J, Blom J, Létisse F, Niehaus K, Goesmann A, Vorhölter FJ. Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris. Microbiology (Reading) 2017; 163:1117-1144. [DOI: 10.1099/mic.0.000473] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Sarah Schatschneider
- Abteilung für Proteom und Metabolomforschung, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Bielefeld, Germany
- Present address: Evonik Nutrition and Care GmbH, Kantstr. 2, 33790 Halle-Künsebeck, Germany
| | - Jessica Schneider
- Bioinformatics Resource Facility, Centrum für Biotechnologie, Universität Bielefeld, Germany
- Present address: Evonik Nutrition and Care GmbH, Kantstr. 2, 33790 Halle-Künsebeck, Germany
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Gießen, Germany
| | - Fabien Létisse
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Karsten Niehaus
- Abteilung für Proteom und Metabolomforschung, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Bielefeld, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus-Liebig-University Gießen, Germany
| | - Frank-Jörg Vorhölter
- Institut für Genomforschung und Systembiologie, Centrum für Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, Germany
- Present address: MVZ Dr. Eberhard & Partner Dortmund, Dortmund, Germany
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8
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Midha S, Bansal K, Kumar S, Girija AM, Mishra D, Brahma K, Laha GS, Sundaram RM, Sonti RV, Patil PB. Population genomic insights into variation and evolution of Xanthomonas oryzae pv. oryzae. Sci Rep 2017; 7:40694. [PMID: 28084432 PMCID: PMC5233998 DOI: 10.1038/srep40694] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 12/08/2016] [Indexed: 11/30/2022] Open
Abstract
Xanthomonas oryzae pv. oryzae ( Xoo) is a serious pathogen of rice causing bacterial leaf blight disease. Resistant varieties and breeding programs are being hampered by the emergence of highly virulent strains. Herein we report population based whole genome sequencing and analysis of 100 Xoo strains from India. Phylogenomic analysis revealed the clustering of Xoo strains from India along with other Asian strains, distinct from African and US Xo strains. The Indian Xoo population consists of a major clonal lineage and four minor but highly diverse lineages. Interestingly, the variant alleles, gene clusters and highly pathogenic strains are primarily restricted to minor lineages L-II to L-V and in particularly to lineage L-III. We could also find the association of an expanded CRISPR cassette and a highly variant LPS gene cluster with the dominant lineage. Molecular dating revealed that the major lineage, L-I is youngest and of recent origin compared to remaining minor lineages that seems to have originated much earlier in the past. Further, we were also able to identify core effector genes that may be helpful in efforts towards building durable resistance against this pathogen.
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Affiliation(s)
- Samriti Midha
- CSIR-Institute of Microbial Technology, Chandigarh, 160036, India
| | - Kanika Bansal
- CSIR-Institute of Microbial Technology, Chandigarh, 160036, India
| | - Sanjeet Kumar
- CSIR-Institute of Microbial Technology, Chandigarh, 160036, India
| | | | - Deo Mishra
- Bayer BioScience Pvt. Ltd., Hyderabad, 500081, India
| | - Kranthi Brahma
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500007, India
| | - Gouri Sankar Laha
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, 500030, India
| | | | - Ramesh V. Sonti
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500007, India
| | - Prabhu B. Patil
- CSIR-Institute of Microbial Technology, Chandigarh, 160036, India
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9
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Draft Genome Sequence of the Xanthan Producer Xanthomonas campestris LMG 8031. GENOME ANNOUNCEMENTS 2016; 4:4/5/e01069-16. [PMID: 27789631 PMCID: PMC5084855 DOI: 10.1128/genomea.01069-16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Here, we report the draft genome sequence of Xanthomonas campestris LMG 8031, for which nearly no genetic information is available, despite its good xanthan-producing properties. We performed an Illumina-based sequencing approach of LMG 8031. The genome revealed a 5.0-Mb chromosome having 4,434 coding sequences and a G+C content of 65%.
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10
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Chen Z, Liu P, Li Z, Yu W, Wang Z, Yao H, Wang Y, Li Q, Deng X, He N. Identification of key genes involved in polysaccharide bioflocculant synthesis in Bacillus licheniformis. Biotechnol Bioeng 2016; 114:645-655. [PMID: 27667128 DOI: 10.1002/bit.26189] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 09/21/2016] [Accepted: 09/23/2016] [Indexed: 11/10/2022]
Abstract
The present study reports the sequenced genome of Bacillus licheniformis CGMCC 2876, which is composed of a 4,284,461 bp chromosome that contains 4,188 protein-coding genes, 72 tRNA genes, and 21 rRNA genes. Additional analysis revealed an eps gene cluster with 16 open reading frames. Conserved Domains Database analysis combined with qPCR experiments indicated that all genes in this cluster were involved in polysaccharide bioflocculant synthesis. Phosphoglucomutase and UDP-glucose pyrophosphorylase were supposed to be key enzymes in polysaccharide secretion in B. licheniformis. A biosynthesis pathway for the production of polysaccharide bioflocculant involving the integration of individual genes was proposed based on functional analysis. Overexpression of epsDEF from the eps gene cluster in B. licheniformis CGMCC 2876 increased the flocculating activity of the recombinant strain by 90% compared to the original strain. Similarly, the crude yield of polysaccharide bioflocculant was enhanced by 27.8%. Overexpression of the UDP-glucose pyrophosphorylase gene not only increased the flocculating activity by 71% but also increased bioflocculant yield by 13.3%. Independent of UDP-N-acetyl-D-mannosamine dehydrogenase gene, flocculating activity, and polysaccharide yield were negatively impacted by overexpression of the UDP-N-acetylglucosamine 2-epimerase gene. Overall, epsDEF and gtaB2 were identified as key genes for polysaccharide bioflocculant synthesis in B. licheniformis. These results will be useful for further engineering of B. licheniformis for industrial bioflocculant production. Biotechnol. Bioeng. 2017;114: 645-655. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Zhen Chen
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, People's Republic of China.,Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, 361005, People's Republic of China
| | - Peize Liu
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, People's Republic of China.,Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, 361005, People's Republic of China
| | - Zhipeng Li
- Fujian Provincial Key Laboratory of Fire Retardant Materials, College of Materials, Xiamen University, Xiamen, People's Republic of China
| | - Wencheng Yu
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, People's Republic of China.,Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, 361005, People's Republic of China
| | - Zhi Wang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, People's Republic of China.,Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, 361005, People's Republic of China
| | - Haosheng Yao
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, People's Republic of China.,Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, 361005, People's Republic of China
| | - Yuanpeng Wang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, People's Republic of China.,Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, 361005, People's Republic of China
| | - Qingbiao Li
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, People's Republic of China.,Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, 361005, People's Republic of China
| | - Xu Deng
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Ning He
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, People's Republic of China.,Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, 361005, People's Republic of China
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11
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Abstract
Escherichia coli JF733 is a strain with a long history in research on membrane proteins and processes. However, tracing back the strain development raises some questions concerning the correct genotype of JF733. Here, we present the complete draft genome of E. coli JF733 in order to resolve any remaining uncertainties.
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12
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Alkhateeb RS, Vorhölter FJ, Rückert C, Mentz A, Wibberg D, Hublik G, Niehaus K, Pühler A. Genome wide transcription start sites analysis of Xanthomonas campestris pv. campestris B100 with insights into the gum gene cluster directing the biosynthesis of the exopolysaccharide xanthan. J Biotechnol 2016; 225:18-28. [PMID: 26975844 DOI: 10.1016/j.jbiotec.2016.03.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Revised: 03/08/2016] [Accepted: 03/10/2016] [Indexed: 01/18/2023]
Abstract
Xanthomonas campestris pv. campestris (Xcc) is the major producer of the exopolysaccharide xanthan, the commercially most important natural polysaccharide of microbial origin. The current work provides deeper insights into the yet uncharacterized transcriptomic features of the xanthan producing strain Xcc-B100. Towards this goal, RNA sequencing of a library based on the selective enrichment of the 5' ends of native transcripts was performed. This approach resulted in the genome wide identification of 3067 transcription start sites (TSSs) that were further classified based on their genomic positions. Among them, 1545 mapped upstream of an actively transcribed CDS and 1363 were classified as novel TSSs representing antisense, internal, and TSSs belonging to previously unidentified genomic features. Analyzing the transcriptional strength of primary and antisense TSSs revealed that in some instances antisense transcription seemed to be initiated at a higher level than its sense counterpart. Mapping the exact positions of TSSs aided in the identification of promoter consensus motifs, ribosomal binding sites, and enhanced the genome annotation of 159 in silico predicted translational start (TLS) sites. The global view on length distribution of the 5' untranslated regions (5'-UTRs) deduced from the data pointed to the occurrence of leaderless transcripts and transcripts with unusually long 5'-UTRs, in addition to identifying seven putative riboswitch elements for Xcc-B100. Concerning the biosynthesis of xanthan, we focused on the transcriptional organization of the gum gene cluster. Under the conditions tested, we present evidence for a complex transcription pattern of the gum genes with multiple TSSs and an obvious considerable role of antisense transcription. The gene gumB, encoding an outer membrane xanthan exporter, is presented here as an example for genes that possessed a strong antisense TSS.
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Affiliation(s)
- Rabeaa S Alkhateeb
- Abteilung für Proteom und Metabolomforschung, Fakultät für Biologie, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Frank-Jörg Vorhölter
- Abteilung für Proteom und Metabolomforschung, Fakultät für Biologie, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, 33615 Bielefeld, Germany; Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Christian Rückert
- Technologie Platform Genomics, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Almut Mentz
- Technologie Platform Genomics, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Daniel Wibberg
- Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Gerd Hublik
- Jungbunzlauer Austria AG, Pernhofen 1, 2064 Wulzeshofen, Austria
| | - Karsten Niehaus
- Abteilung für Proteom und Metabolomforschung, Fakultät für Biologie, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, 33615 Bielefeld, Germany.
| | - Alfred Pühler
- Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, 33615 Bielefeld, Germany
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13
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Ates O. Systems Biology of Microbial Exopolysaccharides Production. Front Bioeng Biotechnol 2015; 3:200. [PMID: 26734603 PMCID: PMC4683990 DOI: 10.3389/fbioe.2015.00200] [Citation(s) in RCA: 160] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 11/30/2015] [Indexed: 11/23/2022] Open
Abstract
Exopolysaccharides (EPSs) produced by diverse group of microbial systems are rapidly emerging as new and industrially important biomaterials. Due to their unique and complex chemical structures and many interesting physicochemical and rheological properties with novel functionality, the microbial EPSs find wide range of commercial applications in various fields of the economy such as food, feed, packaging, chemical, textile, cosmetics and pharmaceutical industry, agriculture, and medicine. EPSs are mainly associated with high-value applications, and they have received considerable research attention over recent decades with their biocompatibility, biodegradability, and both environmental and human compatibility. However, only a few microbial EPSs have achieved to be used commercially due to their high production costs. The emerging need to overcome economic hurdles and the increasing significance of microbial EPSs in industrial and medical biotechnology call for the elucidation of the interrelations between metabolic pathways and EPS biosynthesis mechanism in order to control and hence enhance its microbial productivity. Moreover, a better understanding of biosynthesis mechanism is a significant issue for improvement of product quality and properties and also for the design of novel strains. Therefore, a systems-based approach constitutes an important step toward understanding the interplay between metabolism and EPS biosynthesis and further enhances its metabolic performance for industrial application. In this review, primarily the microbial EPSs, their biosynthesis mechanism, and important factors for their production will be discussed. After this brief introduction, recent literature on the application of omics technologies and systems biology tools for the improvement of production yields will be critically evaluated. Special focus will be given to EPSs with high market value such as xanthan, levan, pullulan, and dextran.
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Affiliation(s)
- Ozlem Ates
- Department of Medical Services and Techniques, Nisantasi University, Istanbul, Turkey
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14
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Genomics and transcriptomics of Xanthomonas campestris species challenge the concept of core type III effectome. BMC Genomics 2015; 16:975. [PMID: 26581393 PMCID: PMC4652430 DOI: 10.1186/s12864-015-2190-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 11/03/2015] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND The bacterial species Xanthomonas campestris infects a wide range of Brassicaceae. Specific pathovars of this species cause black rot (pv. campestris), bacterial blight of stock (pv. incanae) or bacterial leaf spot (pv. raphani). RESULTS In this study, we extended the genomic coverage of the species by sequencing and annotating the genomes of strains from pathovar incanae (CFBP 1606R and CFBP 2527R), pathovar raphani (CFBP 5828R) and a pathovar formerly named barbareae (CFBP 5825R). While comparative analyses identified a large core ORFeome at the species level, the core type III effectome was limited to only three putative type III effectors (XopP, XopF1 and XopAL1). In Xanthomonas, these effector proteins are injected inside the plant cells by the type III secretion system and contribute collectively to virulence. A deep and strand-specific RNA sequencing strategy was adopted in order to experimentally refine genome annotation for strain CFBP 5828R. This approach also allowed the experimental definition of novel ORFs and non-coding RNA transcripts. Using a constitutively active allele of hrpG, a master regulator of the type III secretion system, a HrpG-dependent regulon of 141 genes co-regulated with the type III secretion system was identified. Importantly, all these genes but seven are positively regulated by HrpG and 56 of those encode components of the Hrp type III secretion system and putative effector proteins. CONCLUSIONS This dataset is an important resource to mine for novel type III effector proteins as well as for bacterial genes which could contribute to pathogenicity of X. campestris.
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15
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Schmid J, Sieber V, Rehm B. Bacterial exopolysaccharides: biosynthesis pathways and engineering strategies. Front Microbiol 2015; 6:496. [PMID: 26074894 PMCID: PMC4443731 DOI: 10.3389/fmicb.2015.00496] [Citation(s) in RCA: 300] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 05/06/2015] [Indexed: 12/13/2022] Open
Abstract
Bacteria produce a wide range of exopolysaccharides which are synthesized via different biosynthesis pathways. The genes responsible for synthesis are often clustered within the genome of the respective production organism. A better understanding of the fundamental processes involved in exopolysaccharide biosynthesis and the regulation of these processes is critical toward genetic, metabolic and protein-engineering approaches to produce tailor-made polymers. These designer polymers will exhibit superior material properties targeting medical and industrial applications. Exploiting the natural design space for production of a variety of biopolymer will open up a range of new applications. Here, we summarize the key aspects of microbial exopolysaccharide biosynthesis and highlight the latest engineering approaches toward the production of tailor-made variants with the potential to be used as valuable renewable and high-performance products for medical and industrial applications.
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Affiliation(s)
- Jochen Schmid
- Chair of Chemistry of Biogenic Resources, Technische Universität MünchenStraubing, Germany
| | - Volker Sieber
- Chair of Chemistry of Biogenic Resources, Technische Universität MünchenStraubing, Germany
| | - Bernd Rehm
- Institute of Fundamental Sciences, Massey UniversityPalmerston North, New Zealand
- The MacDiarmid Institute for Advanced Materials and NanotechnologyPalmerston North, New Zealand
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