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Life
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Cyanobacteria: Advances in (Meta-)Genomics and Proteomics
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Cyanobacteria: Advances in (Meta-)Genomics and Proteomics

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Microbiology".

Deadline for manuscript submissions: closed (30 June 2021) | Viewed by 11005

Special Issue Editors

Dr. Paul M. D'Agostino

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Guest Editor
Department of Chemistry and Food Chemistry, Technical University of Dresden, 01062 Dresden, Germany
Interests: natural products; cyanotoxins; synthetic biology; heterologous expression; proteomics; genome mining
Special Issues, Collections and Topics in MDPI journals
Dr. Nádia Eusébio

E-Mail Website
Guest Editor
Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), 4450-208 Matosinhos, Portugal
Interests: natural products; cyanobacteria; halogenases; genetics; microbiology; biotechnology
Special Issues, Collections and Topics in MDPI journals
Dr. Ângela Brito

E-Mail Website
Guest Editor
i3S - Instituto de Investigação e Inovação em Saúde & IBMC – Instituto de Biologia Molecular e Celular, Universidade do Porto, 4150-180 Porto, Portugal
Interests: cyanobacteria; molecular microbiology; comparative genomics; phylogeny; cyanobacterial diversity; natural products; biotechnology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Cyanobacteria are an ancient prokaryote phylum that evolved ~3 billion years ago and are attributed with oxygenating the Earth’s atmosphere during the Great Oxygenation event. Their long evolutionary history has allowed them to evolve a complex metabolic diversity and to occupy many niches within symbiotic, terrestrial, benthic and aquatic environments. Cyanobacteria play significant ecological roles with great prospects for biotechnology, production of lipids for biofuels, bioreactors, wastewater treatment, and biofertilizers, and are prolific producers of structurally intriguing and bioactive natural products, including toxins, sunscreens and potential pharmaceuticals.

The increased accessibility of next-generation sequencing has resulted in an abundance of genome data and led to the wonderful comprehension of cyanobacterial molecular biology, primary and secondary metabolism, as well as phylogeny and evolution. Genomics has further provided a platform for the discovery of natural products using synthetic biology approaches as well as functional proteomics studies to describe how cyanobacteria respond to their external environments. As cyanobacterial genomic and proteomics projects continue to mature, we eagerly await the exciting discoveries these data will provide.

In this Special Issue of Life, we invite researchers from all over the world to share with us their recent advances in the understanding of cyanobacteria at the genomic and proteomic levels. This includes original work and review articles with a focus on (meta-)genomics, phylogenomics, biotechnology, primary and secondary metabolism, genome mining for natural product pathways, comparative -omics and new proteomic discoveries.

Dr. Paul M. D'Agostino
Dr. Nádia Eusébio
Dr. Ângela Brito
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Life is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • genomics
  • metagenomics
  • natural products
  • genome mining
  • cyanotoxins
  • biotechnology
  • secondary metabolism
  • phylogeny
  • comparative genomics
  • proteomics

Published Papers (4 papers)

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Research

8 pages, 1344 KiB  
Communication
CRISPRi as a Tool to Repress Multiple Copies of Extracellular Polymeric Substances (EPS)-Related Genes in the Cyanobacterium Synechocystis sp. PCC 6803
by Marina Santos, Catarina C. Pacheco, Lun Yao, Elton P. Hudson and Paula Tamagnini
Life 2021, 11(11), 1198; https://doi.org/10.3390/life11111198 - 6 Nov 2021
Cited by 7 | Viewed by 2013
Abstract
The use of the versatile cyanobacterial extracellular polymeric substances (EPS) for biotechnological/biomedical applications implies an extensive knowledge of their biosynthetic pathways to improve/control polymer production yields and characteristics. The multiple copies of EPS-related genes, scattered throughout cyanobacterial genomes, adds another layer of complexity, [...] Read more.
The use of the versatile cyanobacterial extracellular polymeric substances (EPS) for biotechnological/biomedical applications implies an extensive knowledge of their biosynthetic pathways to improve/control polymer production yields and characteristics. The multiple copies of EPS-related genes, scattered throughout cyanobacterial genomes, adds another layer of complexity, making these studies challenging and time-consuming. Usually, this issue would be tackled by generating deletion mutants, a process that in cyanobacteria is also hindered by the polyploidy. Thus, the use of the CRISPRi multiplex system constitutes an efficient approach to addressing this redundancy. Here, three putative Synechocystis sp. PCC 6803 kpsM homologues (slr0977, slr2107, and sll0574) were repressed using this methodology. The characterization of the 3-sgRNA mutant in terms of fitness/growth and total carbohydrates, released and capsular polysaccharides, and its comparison with previously generated single knockout mutants pointed towards Slr0977 being the key KpsM player in Synechocystis EPS production. This work validates CRISPRi as a powerful tool to unravel cyanobacterial complex EPS biosynthetic pathways expediting this type of studies. Full article
(This article belongs to the Special Issue Cyanobacteria: Advances in (Meta-)Genomics and Proteomics)
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19 pages, 2151 KiB  
Article
Final Destination? Pinpointing Hyella disjuncta sp. nov. PCC 6712 (Cyanobacteria) Based on Taxonomic Aspects, Multicellularity, Nitrogen Fixation and Biosynthetic Gene Clusters
by Patrick Jung, Paul M. D’Agostino, Katharina Brust, Burkhard Büdel and Michael Lakatos
Life 2021, 11(9), 916; https://doi.org/10.3390/life11090916 - 3 Sep 2021
Cited by 3 | Viewed by 2932
Abstract
Unicellular cyanobacteria inhabit a wide range of ecosytems and can be found throughout the phylum offering space for taxonomic confusion. One example is strain PCC 6712 that was described as Chlorogloea sp. (Nostocales) and later assigned to the genus Chroococcidiopsis (Chroococcidiopsidales). We now [...] Read more.
Unicellular cyanobacteria inhabit a wide range of ecosytems and can be found throughout the phylum offering space for taxonomic confusion. One example is strain PCC 6712 that was described as Chlorogloea sp. (Nostocales) and later assigned to the genus Chroococcidiopsis (Chroococcidiopsidales). We now show that this strain belongs to the order Pleurocapsales and term it Hyella disjuncta based on morphology, genome analyses and 16S-23S ITS rRNA phylogeny. Genomic analysis indicated that H. disjuncta PCC 6712 shared about 44.7% orthologue genes with its closest relative H. patelloides. Furthermore, 12 cryptic biosynthetic gene clusters (BGCs) with potential bioactivity, such as a mycosporine-like amino acid BGC, were detected. Interestingly, the full set of nitrogen fixation genes was found in H. disjuncta PCC 6712 despite its inability to grow on nitrogen-free medium. A comparison of genes responsible for multicellularity was performed, indicating that most of these genes were present and related to those found in other cyanobacterial orders. This is in contrast to the formation of pseudofilaments—a main feature of the genus Hyella—which is weakly expressed in H. disjuncta PCC 6712 but prominent in Hyella patelloides LEGE 07179. Thus, our study pinpoints crucial but hidden aspects of polyphasic cyanobacterial taxonomy. Full article
(This article belongs to the Special Issue Cyanobacteria: Advances in (Meta-)Genomics and Proteomics)
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13 pages, 3126 KiB  
Article
Identification of Putative Biosynthetic Gene Clusters for Tolyporphins in Multiple Filamentous Cyanobacteria
by Xiaohe Jin, Yunlong Zhang, Ran Zhang, Kathy-Uyen Nguyen, Jonathan S. Lindsey and Eric S. Miller
Life 2021, 11(8), 758; https://doi.org/10.3390/life11080758 - 28 Jul 2021
Cited by 7 | Viewed by 2407
Abstract
Tolyporphins A–R are unusual tetrapyrrole macrocycles produced by the non-axenic filamentous cyanobacterium HT-58-2. A putative biosynthetic gene cluster for biosynthesis of tolyporphins (here termed BGC-1) was previously identified in the genome of HT-58-2. Here, homology searching of BGC-1 in HT-58-2 led to identification [...] Read more.
Tolyporphins A–R are unusual tetrapyrrole macrocycles produced by the non-axenic filamentous cyanobacterium HT-58-2. A putative biosynthetic gene cluster for biosynthesis of tolyporphins (here termed BGC-1) was previously identified in the genome of HT-58-2. Here, homology searching of BGC-1 in HT-58-2 led to identification of similar BGCs in seven other filamentous cyanobacteria, including strains Nostoc sp. 106C, Nostoc sp. RF31YmG, Nostoc sp. FACHB-892, Brasilonema octagenarum UFV-OR1, Brasilonema octagenarum UFV-E1, Brasilonema sennae CENA114 and Oculatella sp. LEGE 06141, suggesting their potential for tolyporphins production. A similar gene cluster (BGC-2) also was identified unexpectedly in HT-58-2. Tolyporphins BGCs were not identified in unicellular cyanobacteria. Phylogenetic analysis based on 16S rRNA and a common component of the BGCs, TolD, points to a close evolutionary history between each strain and their respective tolyporphins BGC. Though identified with putative tolyporphins BGCs, examination of pigments extracted from three cyanobacteria has not revealed the presence of tolyporphins. Overall, the identification of BGCs and potential producers of tolyporphins presents a collection of candidate cyanobacteria for genetic and biochemical analysis pertaining to these unusual tetrapyrrole macrocycles. Full article
(This article belongs to the Special Issue Cyanobacteria: Advances in (Meta-)Genomics and Proteomics)
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17 pages, 7083 KiB  
Article
Natural Product Gene Clusters in the Filamentous Nostocales Cyanobacterium HT-58-2
by Xiaohe Jin, Eric S. Miller and Jonathan S. Lindsey
Life 2021, 11(4), 356; https://doi.org/10.3390/life11040356 - 18 Apr 2021
Cited by 5 | Viewed by 2796
Abstract
Cyanobacteria are known as rich repositories of natural products. One cyanobacterial-microbial consortium (isolate HT-58-2) is known to produce two fundamentally new classes of natural products: the tetrapyrrole pigments tolyporphins A–R, and the diterpenoid compounds tolypodiol, 6-deoxytolypodiol, and 11-hydroxytolypodiol. The genome (7.85 Mbp) of [...] Read more.
Cyanobacteria are known as rich repositories of natural products. One cyanobacterial-microbial consortium (isolate HT-58-2) is known to produce two fundamentally new classes of natural products: the tetrapyrrole pigments tolyporphins A–R, and the diterpenoid compounds tolypodiol, 6-deoxytolypodiol, and 11-hydroxytolypodiol. The genome (7.85 Mbp) of the Nostocales cyanobacterium HT-58-2 was annotated previously for tetrapyrrole biosynthesis genes, which led to the identification of a putative biosynthetic gene cluster (BGC) for tolyporphins. Here, bioinformatics tools have been employed to annotate the genome more broadly in an effort to identify pathways for the biosynthesis of tolypodiols as well as other natural products. A putative BGC (15 genes) for tolypodiols has been identified. Four BGCs have been identified for the biosynthesis of other natural products. Two BGCs related to nitrogen fixation may be relevant, given the association of nitrogen stress with production of tolyporphins. The results point to the rich biosynthetic capacity of the HT-58-2 cyanobacterium beyond the production of tolyporphins and tolypodiols. Full article
(This article belongs to the Special Issue Cyanobacteria: Advances in (Meta-)Genomics and Proteomics)
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