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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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da Costa WLO, Araújo CLDA, Dias LM, Pereira LCDS, Alves JTC, Araújo FA, Folador EL, Henriques I, Silva A, Folador ARC. Functional annotation of hypothetical proteins from the Exiguobacterium antarcticum strain B7 reveals proteins involved in adaptation to extreme environments, including high arsenic resistance. PLoS One 2018; 13:e0198965. [PMID: 29940001 PMCID: PMC6016940 DOI: 10.1371/journal.pone.0198965] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 05/28/2018] [Indexed: 02/07/2023] Open
Abstract
Exiguobacterium antarcticum strain B7 is a psychrophilic Gram-positive bacterium that possesses enzymes that can be used for several biotechnological applications. However, many proteins from its genome are considered hypothetical proteins (HPs). These functionally unknown proteins may indicate important functions regarding the biological role of this bacterium, and the use of bioinformatics tools can assist in the biological understanding of this organism through functional annotation analysis. Thus, our study aimed to assign functions to proteins previously described as HPs, present in the genome of E. antarcticum B7. We used an extensive in silico workflow combining several bioinformatics tools for function annotation, sub-cellular localization and physicochemical characterization, three-dimensional structure determination, and protein-protein interactions. This genome contains 2772 genes, of which 765 CDS were annotated as HPs. The amino acid sequences of all HPs were submitted to our workflow and we successfully attributed function to 132 HPs. We identified 11 proteins that play important roles in the mechanisms of adaptation to adverse environments, such as flagellar biosynthesis, biofilm formation, carotenoids biosynthesis, and others. In addition, three predicted HPs are possibly related to arsenic tolerance. Through an in vitro assay, we verified that E. antarcticum B7 can grow at high concentrations of this metal. The approach used was important to precisely assign function to proteins from diverse classes and to infer relationships with proteins with functions already described in the literature. This approach aims to produce a better understanding of the mechanism by which this bacterium adapts to extreme environments and to the finding of targets with biotechnological interest.
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Affiliation(s)
- Wana Lailan Oliveira da Costa
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil
| | - Carlos Leonardo de Aragão Araújo
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil
| | - Larissa Maranhão Dias
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil
| | - Lino César de Sousa Pereira
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil
| | - Jorianne Thyeska Castro Alves
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil
| | - Fabrício Almeida Araújo
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil
| | - Edson Luiz Folador
- Biotechnology Center, Federal University of Paraiba, João Pessoa, Paraíba, Brazil
| | - Isabel Henriques
- Biology Department & CESAM, University of Aveiro, Aveiro, Portugal
| | - Artur Silva
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil
| | - Adriana Ribeiro Carneiro Folador
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil
- * E-mail: ,
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Baraúna RA, Freitas DY, Pinheiro JC, Folador ARC, Silva A. A Proteomic Perspective on the Bacterial Adaptation to Cold: Integrating OMICs Data of the Psychrotrophic Bacterium Exiguobacterium antarcticum B7. Proteomes 2017; 5:proteomes5010009. [PMID: 28248259 PMCID: PMC5372230 DOI: 10.3390/proteomes5010009] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/24/2016] [Accepted: 12/05/2016] [Indexed: 11/30/2022] Open
Abstract
Since the publication of one of the first studies using 2D gel electrophoresis by Patrick H. O’Farrell in 1975, several other studies have used that method to evaluate cellular responses to different physicochemical variations. In environmental microbiology, bacterial adaptation to cold environments is a “hot topic” because of its application in biotechnological processes. As in other fields, gel-based and gel-free proteomic methods have been used to determine the molecular mechanisms of adaptation to cold of several psychrotrophic and psychrophilic bacterial species. In this review, we aim to describe and discuss these main molecular mechanisms of cold adaptation, referencing proteomic studies that have made significant contributions to our current knowledge in the area. Furthermore, we use Exiguobacterium antarcticum B7 as a model organism to present the importance of integrating genomic, transcriptomic, and proteomic data. This species has been isolated in Antarctica and previously studied at all three omic levels. The integration of these data permitted more robust conclusions about the mechanisms of bacterial adaptation to cold.
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Affiliation(s)
- Rafael A Baraúna
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil.
| | - Dhara Y Freitas
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil.
| | - Juliana C Pinheiro
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil.
| | - Adriana R C Folador
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil.
| | - Artur Silva
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil.
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